From hershel.safer at weizmann.ac.il Mon Dec 1 04:13:59 2003 From: hershel.safer at weizmann.ac.il (Hershel Safer) Date: Mon, 1 Dec 2003 11:13:59 +0200 Subject: [BiO BB] Bioinformatics Survey In-Reply-To: <3FC72D2A.275977A5@nottingham.ac.uk> Message-ID: You might also check out the educational offerings at various institutions (both physical and electronic) at www.iscb.org . Hershel On Friday, Nov 28, 2003, at 13:10 Asia/Jerusalem, Natalio Krasnogor wrote: > Dear Colleague, > > I am conducting a webioner (i.e. Web based Questionnaire) with the aim > of capturing recognized researchers and educators views regarding > bioinformatics education in academia. > > The information you input will help me to devise a robust core > bioinformatics curriculum for the School of Computer Science and IT at > the University of Nottingham. > > More specifically, this poll is aimed at trying to understand your > perceptions of what should be included (and what left out) in core > bioinformatics and auxiliary modules, > what skills must be developed in both teachers and learners, etc. > > I would very much appreciate your input as part of my information > gathering efforts. > > The webioner can be found in: > > http://www.cs.nott.ac.uk/~nxk/POLL2/natWebioner.html > > > Thanks in advance for your time and for sharing your expertise. > > Yours, > > Dr. N.Krasnogor > Lecturer > School of Computer Science and Information Technology > University of Nottingham > United Kingdom. > > -- > ----------------------------------------------------------------------- > ----------- > NATALIO KRASNOGOR, Ph.D. Automated Scheduling, Planning and > Optimisation Group > Lecturer School of Computer Sciences and Information > Technology > Jubilee Campus > University of > Nottingham > Tel.: +44 - 0115 - 8467592 Nottingham, NG81BB > United Kingdom > > URL: http://www.cs.nott.ac.uk/~nxk/ > > e-mail: Natalio.Krasnogor-replace all this by at > symbol-nottingham.ac.uk > ----------------------------------------------------------------------- > ----------- > We have recently published a book on Fuzzy Sets, details at > http://www.springer-ny.com/detail.tpl?isbn=354000551X > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > -------------------------------------------------- ** Putting the "bio" back into bioinformatics ** The world's biggest and broadest bioinformatics conference! ** ISMB/ECCB 2004 will be held in Glasgow, Scotland, UK ** From 31 July - 4 August 2004 ** For more information, visit http://www.iscb.org/ismbeccb2004 Hershel M. Safer, Ph.D. Head, Bioinformatics and Biological Computing Weizmann Institute of Science PO Box 26, Rehovot 76100, Israel Tel: +972-8-934-3456 Fax: +972-8-934-6006 Email: Hershel.Safer at weizmann.ac.il URL: http://bip.weizmann.ac.il From dmb at mrc-dunn.cam.ac.uk Mon Dec 1 06:30:41 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 1 Dec 2003 11:30:41 -0000 (GMT) Subject: [BiO BB] Final Call: Data Integration in the Life Sciences, DILS04 In-Reply-To: <3FBA5859.5060503@izbi.uni-leipzig.de> References: <3FBA5859.5060503@izbi.uni-leipzig.de> Message-ID: <35420.80.4.6.169.1070278241.squirrel@www.mrc-dunn.cam.ac.uk> Dear Sir/Madam, I am having trouble meeting the deadline, but I believe my paper is very relevant to the conference. I would like to ask if I can still send my paper in the next couple of days? Below I have reproduced the abstract. I would be very grateful if you could consider this paper for submission in a couple of days. Yours sincerely, Dan Bolser. Abstract A major challenge in the post-genomic era is the integration, classification and dissemination of of diverse sources of biological data. Data integration is attractive for several reasons, providing context for biological analysis, allowing different types of data to be cross-correlated, and providing a validation framework for different sources of experimentally and computationally derived data. Centralised data repositories have proven very effective at organising specific kinds of data, both helping to coordinate the research community and providing standards for the categorisation and distribution of the accumulated knowledge. However, the underlying conceptual complexity of data in the biological domain, as well as the continual development of new concepts, makes the task of producing a 'universal' data repository much more challenging. As a consequence many integrated databases have become arbitrarily complex, with no intrinsic classification value. Here, we emphasise a point which is not widely acknowledged by the database community, that data modelling in the scientific domain is equivalent to the scientific process itself. To this end we propose a 'distributed data model' framework for data integration in the scientific domain. Different sources of data to be integrated with will naturally have conceptual overlap (if they are to be integrated at all), but may have very complex conceptual and/or algorithmic associations. In this framework the burden of integration is put back on the domain expert (to implement or devise specific integration strategies), but the underlying issues of data access and subsequent distribution are made transparent via the data model framework. The advantage of integrating and distributing data within this framework is that new data and new concepts (produced as the result of integrative analysis for example) are naturally accommodated by specific extensions to the data models of the underlying data. Here we develop components of a high level data model relating to the principal axes of an integrated protein classification database (called the protein periodic table). Additionally we have developed conceptually clear ORM style models for integrated protein interaction data and metabolic pathway data (suitable for metabolic reconstruction). The the subsequent analysis of these models highlights several key areas for model development, and thus highlights areas for scientific research into specific integration and classification techniques. > Final CALL FOR PAPERS > Int. Workshop on Data Integration in the Life Sciences (DILS 2004) > > Deadline: Nov. 30, 2003 > Industrial exhibits welcome > Proceedings will be published in Springer LNCS > > http://izbi.uni-leipzig.de/dils04 > > Workshop date: March 25-26, 2004, Univ. of Leipzig, Germany > ------------------------------------------------------- > AIM AND SCOPE > New advances in life sciences, e.g. molecular biology, > biodiversity, drug discovery and medical research, > increasingly depend on bioinformatics methods to manage > and analyze vast amounts of highly diverse data. > The volume of data is increasing at an unprecedented pace, > fueled by world-wide research activities producing publicly > available data, and new technologies, e.g. high-throughput > devices such as microarrays. Thus, data mining and analysis > require comprehensive integration of heterogeneous data, > that is typically distributed across many data sources > on the web and often structured only to a limited extent. > Despite new interoperability technologies such as XML and > web services, data integration is a highly difficult and > still largely manual task, especially due to the high > degree of semantic heterogeneity and varying data quality > as well as specific application requirements. > > DILS 2004 aims at providing a new forum for > presenting novel research results and assessing > the state of the art in the field of data integration > for life sciences. It addresses researchers, > professionals, and industrial practitioners to > share their knowledge on this highly important > bioinformatics subject. > > In an effort to bring together academics and industrial > practitioners, we solicit both research papers and > application / experience papers. It is planned to > publish accepted papers by Springer-Verlag in the > Lecture Notes in Computer Science (LNCS) series. > > TOPICS OF INTEREST > Topics of interest include, but are not limited to: > * Challenges for data integration in life sciences > * Architectures for data integration in life sciences > * Ontology-based data integration and analysis > * Metadata and annotation management > * Data quality and data cleaning > * Tool integration and experimental workflows > * Evaluation of data integration approaches in life sciences > * Data integration for specific applications > * Prototypes and commercial solutions > > PAPER SUBMISSION > Authors are invited to submit original, previously > unpublished papers. All submitted papers will be > peer-refereed for quality, correctness, originality > and relevance. Accepted papers will be published in > the workshop proceedings which will be available > at the workshop. > > Submissions must not exceed 15 pages and should be > formatted according to the LNCS guidelines under: > http://www.springer.de/comp/lncs/authors.html > All submissions will be handled electronically. > Please send your submissions in PDF format to > dils04 at izbi.uni-leipzig.de > Please also visit the workshop website for further > information http://izbi.uni-leipzig.de/dils04 > > IMPORTANT DATES > Paper submissions: November 30, 2003 > Author notification: January 8, 2004 > Camera-ready due: January 28, 2004 > Workshop date: March 25-26, 2004 > > WORKSHOP CHAIR > Erhard Rahm, Univ. of Leipzig > > PROGRAM COMMITTEE > > Howard Bilofsky, GlaxoSmithKline, USA > Terence Critchlow, Lawrence Livermore National Laboratory, USA > Peter Gray, Univ. of Aberdeen, UK > Barbara Heller, Univ. of Leipzig, Germany > Ralf Hofestaedt, Univ. of Bielefeld, Germany > Jessie Kennedy, Napier Univ. Edinburgh, UK > Ulf Leser, HU Berlin, Germany > Bertram Lud?scher, San Diego Supercomputer Center, USA > Sergey Melnik, Microsoft Research, USA > Peter Mork, Univ. of Washington, Seattle, USA > Felix Naumann, HU Berlin, Germany > Frank Olken, Lawrence Berkeley National Laboratory, USA > Norman Paton, Univ. of Manchester, UK > Erhard Rahm, Univ. of Leipzig, Germany > Louiqa Raschid, Univ. of Maryland, USA > Kai-Uwe Sattler, TU Ilmenau, Germany > Steffen Schulze-Kremer, FU Berlin, Germany > Robert Stevens, Univ. of Manchester, UK > Sharon Wang, IBM Life Sciences, USA > Limsoon Wong, Institute for Infocomm Research, Singapore > > EXHIBITION > Sponsors of the event can exhibit their software > and other products. > > ORGANIZATION > The workshop is organized by the Bioinformatics centre > of the University of Leipzig (www.izbi.de). > ------------------------------- > Prof. Dr. Erhard Rahm > http://dbs.uni-leipzig.de > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Mon Dec 1 06:33:40 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 1 Dec 2003 11:33:40 -0000 (GMT) Subject: [BiO BB] Bioinformatics Survey: +2 In-Reply-To: <20031130115914.A1384@lifebook> References: <3FC72D2A.275977A5@nottingham.ac.uk> <3FCA2A67.AB207C1C@utoronto.ca> <20031130115914.A1384@lifebook> Message-ID: <35472.80.4.6.169.1070278420.squirrel@www.mrc-dunn.cam.ac.uk> > Hi, Boris Steipe ! > > On Sun, Nov 30, 2003 at 12:35:35PM -0500, Boris Steipe wrote: > >> Natalio Krasnogor wrote: >> > >> > Dear Colleague, >> > >> > I am conducting a webioner (i.e. Web based Questionnaire) with the aim of >> capturing recognized researchers and educators views regarding bioinformatics >> education in academia. >> [...] >> >> I would be willing to participate if you would pledge to make the results of the >> survey available, either publically, or at least to those participating in the >> survey. >> >> I am sure this would be of interest and value to many who are subscribed here. > > I agree. Sounds good. > > Best regards, > > -- > DIG (Dmitri I GOULIAEV) http://www.bioinformatics.org/~dig/ 1024D/63A6C649: > 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From dmb at mrc-dunn.cam.ac.uk Mon Dec 1 06:53:32 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Mon, 1 Dec 2003 11:53:32 -0000 (GMT) Subject: [BiO BB] Final Call: Data Integration in the Life Sciences, DILS04 In-Reply-To: <35420.80.4.6.169.1070278241.squirrel@www.mrc-dunn.cam.ac.uk> References: <3FBA5859.5060503@izbi.uni-leipzig.de> <35420.80.4.6.169.1070278241.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <35749.80.4.6.169.1070279612.squirrel@www.mrc-dunn.cam.ac.uk> oops... ;) > > Dear Sir/Madam, > > I am having trouble meeting the deadline, but I believe my paper is very relevant > to the conference. I would like to ask if I can still send my paper in the next > couple of days? > > Below I have reproduced the abstract. > > I would be very grateful if you could consider this paper for submission in a > couple of days. > > Yours sincerely, > Dan Bolser. > > Abstract > A major challenge in the post-genomic era is the integration, classification and > dissemination of of diverse sources of biological data. Data integration is > attractive for several reasons, providing context for biological analysis, > allowing different types of data to be cross-correlated, and providing a > validation framework for different sources of experimentally and computationally > derived data. Centralised data repositories have proven very effective at > organising specific kinds of data, both helping to coordinate the research > community and providing standards for the categorisation and distribution of the > accumulated knowledge. However, the underlying conceptual complexity of data in > the biological domain, as well as the continual development of new concepts, makes > the task of producing a 'universal' data repository much more challenging. As a > consequence many integrated databases have become arbitrarily complex, with no > intrinsic classification value. > > Here, we emphasise a point which is not widely acknowledged by the database > community, that data modelling in the scientific domain is equivalent to the > scientific process itself. To this end we propose a 'distributed data model' > framework for data integration in the scientific domain. Different sources of data > to be integrated with will naturally have conceptual overlap (if they are to be > integrated at all), but may have very complex conceptual and/or algorithmic > associations. In this framework the burden of integration is put back on the > domain expert (to implement or devise specific integration strategies), but the > underlying issues of data access and subsequent distribution are made transparent > via the data model framework. The advantage of integrating and distributing data > within this framework is that new data and new concepts (produced as the result of > integrative analysis for example) are naturally accommodated by specific > extensions to the data models of the underlying data. > > Here we develop components of a high level data model relating to the principal > axes of an integrated protein classification database (called the protein periodic > table). Additionally we have developed conceptually clear ORM style models for > integrated protein interaction data and metabolic pathway data (suitable for > metabolic reconstruction). The the subsequent analysis of these models highlights > several key areas for model development, and thus highlights areas for scientific > research into specific integration and classification techniques. > > > > >> Final CALL FOR PAPERS >> Int. Workshop on Data Integration in the Life Sciences (DILS 2004) >> >> Deadline: Nov. 30, 2003 >> Industrial exhibits welcome >> Proceedings will be published in Springer LNCS >> >> http://izbi.uni-leipzig.de/dils04 >> >> Workshop date: March 25-26, 2004, Univ. of Leipzig, Germany >> ------------------------------------------------------- >> AIM AND SCOPE >> New advances in life sciences, e.g. molecular biology, >> biodiversity, drug discovery and medical research, >> increasingly depend on bioinformatics methods to manage >> and analyze vast amounts of highly diverse data. >> The volume of data is increasing at an unprecedented pace, >> fueled by world-wide research activities producing publicly >> available data, and new technologies, e.g. high-throughput >> devices such as microarrays. Thus, data mining and analysis >> require comprehensive integration of heterogeneous data, >> that is typically distributed across many data sources >> on the web and often structured only to a limited extent. >> Despite new interoperability technologies such as XML and >> web services, data integration is a highly difficult and >> still largely manual task, especially due to the high >> degree of semantic heterogeneity and varying data quality >> as well as specific application requirements. >> >> DILS 2004 aims at providing a new forum for >> presenting novel research results and assessing >> the state of the art in the field of data integration >> for life sciences. It addresses researchers, >> professionals, and industrial practitioners to >> share their knowledge on this highly important >> bioinformatics subject. >> >> In an effort to bring together academics and industrial >> practitioners, we solicit both research papers and >> application / experience papers. It is planned to >> publish accepted papers by Springer-Verlag in the >> Lecture Notes in Computer Science (LNCS) series. >> >> TOPICS OF INTEREST >> Topics of interest include, but are not limited to: >> * Challenges for data integration in life sciences >> * Architectures for data integration in life sciences >> * Ontology-based data integration and analysis >> * Metadata and annotation management >> * Data quality and data cleaning >> * Tool integration and experimental workflows >> * Evaluation of data integration approaches in life sciences >> * Data integration for specific applications >> * Prototypes and commercial solutions >> >> PAPER SUBMISSION >> Authors are invited to submit original, previously >> unpublished papers. All submitted papers will be >> peer-refereed for quality, correctness, originality >> and relevance. Accepted papers will be published in >> the workshop proceedings which will be available >> at the workshop. >> >> Submissions must not exceed 15 pages and should be >> formatted according to the LNCS guidelines under: >> http://www.springer.de/comp/lncs/authors.html >> All submissions will be handled electronically. >> Please send your submissions in PDF format to >> dils04 at izbi.uni-leipzig.de >> Please also visit the workshop website for further >> information http://izbi.uni-leipzig.de/dils04 >> >> IMPORTANT DATES >> Paper submissions: November 30, 2003 >> Author notification: January 8, 2004 >> Camera-ready due: January 28, 2004 >> Workshop date: March 25-26, 2004 >> >> WORKSHOP CHAIR >> Erhard Rahm, Univ. of Leipzig >> >> PROGRAM COMMITTEE >> >> Howard Bilofsky, GlaxoSmithKline, USA >> Terence Critchlow, Lawrence Livermore National Laboratory, USA >> Peter Gray, Univ. of Aberdeen, UK >> Barbara Heller, Univ. of Leipzig, Germany >> Ralf Hofestaedt, Univ. of Bielefeld, Germany >> Jessie Kennedy, Napier Univ. Edinburgh, UK >> Ulf Leser, HU Berlin, Germany >> Bertram Lud?scher, San Diego Supercomputer Center, USA >> Sergey Melnik, Microsoft Research, USA >> Peter Mork, Univ. of Washington, Seattle, USA >> Felix Naumann, HU Berlin, Germany >> Frank Olken, Lawrence Berkeley National Laboratory, USA >> Norman Paton, Univ. of Manchester, UK >> Erhard Rahm, Univ. of Leipzig, Germany >> Louiqa Raschid, Univ. of Maryland, USA >> Kai-Uwe Sattler, TU Ilmenau, Germany >> Steffen Schulze-Kremer, FU Berlin, Germany >> Robert Stevens, Univ. of Manchester, UK >> Sharon Wang, IBM Life Sciences, USA >> Limsoon Wong, Institute for Infocomm Research, Singapore >> >> EXHIBITION >> Sponsors of the event can exhibit their software >> and other products. >> >> ORGANIZATION >> The workshop is organized by the Bioinformatics centre >> of the University of Leipzig (www.izbi.de). >> ------------------------------- >> Prof. Dr. Erhard Rahm >> http://dbs.uni-leipzig.de >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From MEC at Stowers-Institute.org Mon Dec 1 10:31:44 2003 From: MEC at Stowers-Institute.org (Cook, Malcolm) Date: Mon, 1 Dec 2003 09:31:44 -0600 Subject: [BiO BB] QBLAST Message-ID: Dear Yong Huang, Thank you for taking the time to reply to my inquiry. Do I understand correctly? Have you written code which performs blasts by talking to the NCBI's qBlast server? If so, then your code is not helpful to me. I am looking for an implementation of the Qblast server itself. I am running programs that know already how to talk to a QBlast server. I want to point those programs to my own, in-house server. If not, and you have implemented a blast server accordinag to the Qblast protocol, then I am still very interested and would like to hear more. Again, thanks for your time... Regards, Malcolm -----Original Message----- From: yhuang4 at memphis.edu [mailto:yhuang4 at memphis.edu] Sent: Wednesday, November 26, 2003 8:48 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] QBLAST Dear Malcolm, i just saw your post about QBLAST on Sep 2003. I wrote code for batch BLAST through QBLAST at begining of this year (my Master project of bioinformatics). The code was written in JAVA and Perl (Bioperl). The flexibility of the code is: 0.good for single query or batch queries, BLASTn and BLASTp 1. observe the length of the first sequence of the batch queries, and automatically decide the parameters 2.dynamically check the working process 3.output format: HTML XML, Text 4.parse the result (Bioperl)and extraxt info by the user, e.g. top 1, or 2.. hit. If you are still interested in QBLAST, please contact me. Yong Huang Feinstone center for genomic research University of Memphis (901) 678 2458 Email: yhuang4 at memphis.edu _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From yhuang4 at memphis.edu Mon Dec 1 11:26:32 2003 From: yhuang4 at memphis.edu (yhuang4 at memphis.edu) Date: Mon, 01 Dec 2003 10:26:32 -0600 Subject: [BiO BB] QBLAST Message-ID: <3e03203e37cb.3e37cb3e0320@memphis.edu> Dear Malcolm, my code submit batch queries to NCBI~{!/~}s server, check working process. If the result is available, download the result (JAVA code until here), then parse the result and output info according to the user (Bioperl for parsing). I understand my code is not useful for your purpose. Good luck for your project. Yong ----- Original Message ----- From: "Cook, Malcolm" Date: Monday, December 1, 2003 9:31 am Subject: RE: [BiO BB] QBLAST > Dear Yong Huang, > > Thank you for taking the time to reply to my inquiry. > > Do I understand correctly? Have you written code which performs > blastsby talking to the NCBI's qBlast server? > > If so, then your code is not helpful to me. I am looking for an > implementation of the Qblast server itself. I am running programs > thatknow already how to talk to a QBlast server. I want to point > thoseprograms to my own, in-house server. > > If not, and you have implemented a blast server accordinag to the > Qblastprotocol, then I am still very interested and would like to > hear more. > > Again, thanks for your time... > > Regards, > > Malcolm > > > -----Original Message----- > From: yhuang4 at memphis.edu [mailto:yhuang4 at memphis.edu] > Sent: Wednesday, November 26, 2003 8:48 AM > To: bio_bulletin_board at bioinformatics.org > Subject: [BiO BB] QBLAST > > > Dear Malcolm, > i just saw your post about QBLAST on Sep 2003. I wrote code for > batch > BLAST through QBLAST at begining of this year (my Master project > of > bioinformatics). The code was written in JAVA and Perl (Bioperl). > > The flexibility of the code is: > 0.good for single query or batch queries, BLASTn and BLASTp > 1. observe the length of the first sequence of the batch queries, > and > automatically decide the parameters > 2.dynamically check the working process > 3.output format: HTML XML, Text > 4.parse the result (Bioperl)and extraxt info by the user, e.g. top > 1, > or 2.. hit. > > If you are still interested in QBLAST, please contact me. > > > Yong Huang > Feinstone center for genomic research > University of Memphis > (901) 678 2458 > Email: yhuang4 at memphis.edu > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From kard at extremezone.com Tue Dec 2 16:02:40 2003 From: kard at extremezone.com (Spencer Covington) Date: Tue, 2 Dec 2003 14:02:40 -0700 Subject: [BiO BB] Blue Gene/L Message-ID: <002a01c3b917$a4361520$529e8c40@computer> My school ( Arizona State University ) has recently acquired a supercomputer ( an IBM Blue Gene/L ). I am preparing to begin a M.S. in Computational Bioscience ( Genomics / Bioinformatics ) in the fall. Would like to design a project to run on this computer. What kinds of projects should I consider ? Spencer Covington -------------- next part -------------- An HTML attachment was scrubbed... URL: From boris.steipe at utoronto.ca Tue Dec 2 16:47:29 2003 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Tue, 02 Dec 2003 16:47:29 -0500 Subject: [BiO BB] Blue Gene/L References: <002a01c3b917$a4361520$529e8c40@computer> Message-ID: <3FCD086F.6929057F@utoronto.ca> > Spencer Covington wrote: > > My school ( Arizona State University ) has recently acquired a supercomputer ( > an IBM Blue Gene/L ). I am preparing to begin a M.S. in Computational > Bioscience ( Genomics / Bioinformatics ) in the fall. Would like to design a > project to run on this computer. What kinds of projects should I consider ? I find this quite amusing. This almost sounds like a troll: multi-million $$$ solution, deprecating at a significant perecentage each month, waiting for a problem. I've heard similar machines play wicked chess though. Seriously: think about a project to improve MM-forcefields for partially folded proteins with an aim to improve the radius of convergence in folding simulations. This is a problem that has - an objective function that is hard to compute ( radius of convergence is essentially the largest RMSD which you may be off from the native structure and still find it through minimization, i.e. not combinatorial search) - yet parallelizes well across processors - raises interesting issues in combinatorial optimization - has important applications - and needs to keep a lot of stuff in memory at the same time (explicit solvent, atoms etc.) and thus is probably not well suited for distributed applications. Best regards, Boris --- Prof. Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe From dmb at mrc-dunn.cam.ac.uk Thu Dec 4 12:10:19 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 4 Dec 2003 17:10:19 -0000 (GMT) Subject: [BiO BB] Biological Database Journal? In-Reply-To: <3FC72D2A.275977A5@nottingham.ac.uk> References: <3FC72D2A.275977A5@nottingham.ac.uk> Message-ID: <38103.193.60.81.207.1070557819.squirrel@www.mrc-dunn.cam.ac.uk> How can we start a journal? I think there is a gap in the market for a technical journal of biological database. While there are many 'database journals' there is no central repository for database schema or datamodels. i.e. all the models which have been published exist 'out there' in the literature and on various websites as gif images. The NAR database issue is really great, but it would be nice to have a categorized repository to go with it. Additionally, we need a central database of biological datamodels and database schema for example based around http://www.schemamania.org/ Just like the PDB, publishing a database could depend on a valid schema entry in this central database. The accompanying journal would be a place for new technical discoveries relevant to the field to be published, as well as a place to discuss details of specific models. This would be an ideal way to get the community focused on the 'semantic interoperability' problem (sorry to those of you out there who already are :) It would also provide an exelent benchmark for all the integration technologies which exist, giving them a common set of databases to look at. How do you go about starting a journal? Have I totally missed some similar resource? Cheers, Dan. From 1202ab013 at cdl.msitprogram.net Fri Dec 5 11:33:49 2003 From: 1202ab013 at cdl.msitprogram.net (Radhika Tallamraju) Date: Fri, 5 Dec 2003 22:03:49 +0530 (IST) Subject: [BiO BB] help regarding MEME program Message-ID: <1758.172.16.8.66.1070642029.squirrel@cdl.msitprogram.net> Can anyone suggest me how to construct log odds matrix for a given consensus sequence. I need this to run MAST program. Regards, Radhika. From idoerg at burnham.org Fri Dec 5 12:27:38 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 05 Dec 2003 09:27:38 -0800 Subject: [BiO BB] help regarding MEME program In-Reply-To: <1758.172.16.8.66.1070642029.squirrel@cdl.msitprogram.net> References: <1758.172.16.8.66.1070642029.squirrel@cdl.msitprogram.net> Message-ID: <3FD0C00A.2020300@burnham.org> Hi, Biopython provids a pretty generic way of generating log odd matrices. You'll need to download & install it from: http://biopython.org Take a look first at the documentation, see if that is what you are looking for: http://biopython.org/docs/tutorial/Tutorial005.html#toc25 Cheers, ./I Radhika Tallamraju wrote: > Can anyone suggest me how to construct log odds matrix for a given > consensus sequence. I need this to run MAST program. > > Regards, > Radhika. > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From rong at bu.edu Fri Dec 5 13:20:29 2003 From: rong at bu.edu (Rong Chen) Date: Fri, 5 Dec 2003 13:20:29 -0500 (EST) Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: <1758.172.16.8.66.1070642029.squirrel@cdl.msitprogram.net> Message-ID: Hi, Normally, we align a profile against a sequence database in psi-blast. I heard that we could also cat all profiles to create a database, and align a sequence against this profile database. Did anyone hear anything about it? Is it a new program or a new option in psi-blast? Thank you. Rong ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Rong Chen, Ph.D. Scientist Protein Engineering Accelrys Inc. San Diego, CA 92121 Tel: (858)799-5304(office) E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From idoerg at burnham.org Fri Dec 5 13:35:04 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 05 Dec 2003 10:35:04 -0800 Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: References: Message-ID: <3FD0CFD8.6020807@burnham.org> FFAS does this. Was published in: L. Rychlewski, L. Jaroszewski, W. Li, A. Godzik (2000), Protein Science 9, 232-241 (Actually the article refers to an older version of FFAS. The method of the new one is currently in press. But they both do profile-profile alignments). You can access the server at: http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl Cheers, Iddo Rong Chen wrote: > Hi, > > Normally, we align a profile against a sequence database in psi-blast. I > heard that we could also cat all profiles to create a database, and align > a sequence against this profile database. Did anyone hear anything about > it? Is it a new program or a new option in psi-blast? > > Thank you. > > Rong > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Rong Chen, Ph.D. > Scientist > Protein Engineering > Accelrys Inc. > San Diego, CA 92121 > Tel: (858)799-5304(office) > E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From idoerg at burnham.org Fri Dec 5 13:49:38 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 05 Dec 2003 10:49:38 -0800 Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: References: Message-ID: <3FD0D342.9050302@burnham.org> Slight correction: FFAS aligns a /profile/ against a profile database, not a /sequence/ against a profile database. More sensitive that way. ./I Rong Chen wrote: > Hi, > > Normally, we align a profile against a sequence database in psi-blast. I > heard that we could also cat all profiles to create a database, and align > a sequence against this profile database. Did anyone hear anything about > it? Is it a new program or a new option in psi-blast? > > Thank you. > > Rong > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Rong Chen, Ph.D. > Scientist > Protein Engineering > Accelrys Inc. > San Diego, CA 92121 > Tel: (858)799-5304(office) > E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From rong at bu.edu Fri Dec 5 14:40:19 2003 From: rong at bu.edu (Rong Chen) Date: Fri, 5 Dec 2003 14:40:19 -0500 (EST) Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: <3FD0CFD8.6020807@burnham.org> Message-ID: Hi Iddo, In genomic annotation, we normally create a profiles for each sequence in the genome, and align these profiles against some databases (such as PDB) to get annotation. What we found is combine this forward search with a reverse search helped a lot in detecting remote homologies. The reverse search means that we create a profile for each sequence in the databases (PDB) and align each profile against your genome database. Since depending on whether the profile is generated from a query sequence or a template sequence, the sequence profile covers different sequence space. Therefore, combining direct search with reverse search can increase sensitivity. However, when there is only a small number of sequences you want to query, we still need to align each profile of PDB against the databases composed of your target sequences. If we can combine all profiles of PDB into a database, and align your target sequences against this profile databases, we can save a lot of computation time. I heard that new Psi-blast has this reverse search function, but I could not find it in NCBI's website. Did you hear anyting about it? Thank you. Rong On Fri, 5 Dec 2003, Iddo Friedberg wrote: > FFAS does this. > > Was published in: > L. Rychlewski, L. Jaroszewski, W. Li, A. Godzik (2000), Protein Science > 9, 232-241 > (Actually the article refers to an older version of FFAS. The method of > the new one is currently in press. But they both do profile-profile > alignments). > > You can access the server at: > > http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl > > Cheers, > > Iddo > > > Rong Chen wrote: > > Hi, > > > > Normally, we align a profile against a sequence database in psi-blast. I > > heard that we could also cat all profiles to create a database, and align > > a sequence against this profile database. Did anyone hear anything about > > it? Is it a new program or a new option in psi-blast? > > > > Thank you. > > > > Rong > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > Rong Chen, Ph.D. > > Scientist > > Protein Engineering > > Accelrys Inc. > > San Diego, CA 92121 > > Tel: (858)799-5304(office) > > E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > From mgollery at unr.edu Fri Dec 5 14:42:39 2003 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 5 Dec 2003 11:42:39 -0800 Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: References: Message-ID: <1070653359.3fd0dfaf8e95e@webmail.unr.edu> Rong, This is called RPS-BLAST. You can run this locally, or use it on the NCBI website. They have a database called CDD that is a great combination of Pfam, Smart and COG. The psi-blast format is pretty good, considering the speed that you get out of it! Marty Quoting Rong Chen : > Hi, > > Normally, we align a profile against a sequence database in psi-blast. I > heard that we could also cat all profiles to create a database, and align > a sequence against this profile database. Did anyone hear anything about > it? Is it a new program or a new option in psi-blast? > > Thank you. > > Rong > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Rong Chen, Ph.D. > Scientist > Protein Engineering > Accelrys Inc. > San Diego, CA 92121 > Tel: (858)799-5304(office) > E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From idoerg at burnham.org Fri Dec 5 16:17:23 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Fri, 05 Dec 2003 13:17:23 -0800 Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: References: Message-ID: <3FD0F5E3.2020108@burnham.org> I think that Martin's answer covers that. Rong Chen wrote: > Hi Iddo, > > In genomic annotation, we normally create a profiles for each sequence in > the genome, and align these profiles against some databases (such as PDB) > to get annotation. What we found is combine this forward search with a > reverse search helped a lot in detecting remote homologies. The reverse > search means that we create a profile for each sequence in the databases > (PDB) and align each profile against your genome database. Since depending > on whether the profile is generated from a query sequence or a template > sequence, the sequence profile covers different sequence space. Therefore, > combining direct search with reverse search can increase sensitivity. > However, when there is only a small number of sequences you want to query, > we still need to align each profile of PDB against the databases composed > of your target sequences. If we can combine all profiles of PDB into a > database, and align your target sequences against this profile databases, > we can save a lot of computation time. I heard that new Psi-blast has this > reverse search function, but I could not find it in NCBI's website. Did > you hear anyting about it? > > Thank you. > > Rong > > > On Fri, 5 Dec 2003, Iddo Friedberg wrote: > > >>FFAS does this. >> >>Was published in: >>L. Rychlewski, L. Jaroszewski, W. Li, A. Godzik (2000), Protein Science >>9, 232-241 >>(Actually the article refers to an older version of FFAS. The method of >>the new one is currently in press. But they both do profile-profile >>alignments). >> >>You can access the server at: >> >>http://ffas.ljcrf.edu/ffas-cgi/cgi/ffas.pl >> >>Cheers, >> >>Iddo >> >> >>Rong Chen wrote: >> >>>Hi, >>> >>>Normally, we align a profile against a sequence database in psi-blast. I >>>heard that we could also cat all profiles to create a database, and align >>>a sequence against this profile database. Did anyone hear anything about >>>it? Is it a new program or a new option in psi-blast? >>> >>>Thank you. >>> >>>Rong >>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>>Rong Chen, Ph.D. >>>Scientist >>>Protein Engineering >>>Accelrys Inc. >>>San Diego, CA 92121 >>>Tel: (858)799-5304(office) >>>E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong >>>~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >>> >>> >>>_______________________________________________ >>>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >>> >>> >> >> > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From hra at cs.uga.edu Fri Dec 5 19:26:49 2003 From: hra at cs.uga.edu (Hamid Arabnia) Date: Fri, 5 Dec 2003 19:26:49 -0500 (EST) Subject: [BiO BB] 18 Joint Conferences in CS & CE: June 2004, Las Vegas, USA Message-ID: <200312060026.TAA13069@apollo.cs.uga.edu> CALL FOR PAPERS The 2004 International Multiconference in Computer Science and Computer Engineering (18 Joint Int'l Conferences) http://www.world-academy-of-science.org Monte Carlo Resort, Las Vegas, Nevada, USA June 21-24, 2004 Dear Colleagues: You are invited to submit a draft paper (see instructions below) and/or a proposal to organize a technical session/workshop. All accepted papers will be published in the respective conference proceedings. The names of technical session/workshop organizers/chairs will appear on the cover of the proceedings as Associate Editors. Any help in distributing this announcement would be most appreciated. The International Multiconference in Computer Science and Computer Engineering is a major annual research event. It assembles a spectrum of affiliated research conferences into a coordinated research meeting held in a common place at a common time. This model facilitates communication among researchers in different fields of computer science and computer engineering. The last Multiconference attracted over 1,650 computer science and engineering researchers from 78 countries. We expect to have over 2,000 attendees for this set of conference. The 2004 event is composed of the following 18 conferences: 1. The 2004 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'04) 2. The 2004 International Conference on Artificial Intelligence (IC-AI'04) 3. The 2004 International Conference on Imaging Science, Systems, and Technology (CISST'04) 4. The 2004 International Conference on Modeling, Simulation and Visualization Methods (MSV'04) 5. The 2004 International Conference on Software Engineering Research and Practice (SERP'04) 6. The 2004 International Conference on Information and Knowledge Engineering (IKE'04) 7. The 2004 International Conference on Embedded Systems and Applications (ESA'04) 8. The 2004 International Conference on Internet Computing (IC'04) 9. The 2004 International Conference on Wireless Networks (ICWN'04) 10. The 2004 International Symposium on Web Services and Applications (ISWS'04) 11. The 2004 International Conference on Pervasive Computing and Communications (PCC'04) 12. The 2004 International Conference on Security and Management (SAM'04) 13. The 2004 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'04) 14. The 2004 International Conference on Machine Learning; Models, Technologies and Applications (MLMTA'04) 15. The 2004 International Conference on Communications in Computing (CIC'04) 16. The 2004 International Conference on VLSI (VLSI'04) 17. The 2004 International Conference on Engineering of Reconfigurable Systems and Algorithms (ERSA'04) 18. The 2004 International Conference on Algorithmic Mathematics and Computer Science (AMCS'04) (a link to each conference's URL can be found at http://www.world-academy-of-science.org ) Please regard this announcement as General Guidelines. You are requested to send your submission to the Multiconference chair whose address appears below (The chair may be forwarding the papers to respective conference chairs/committees). CONFERENCES CONTACT: H. R. Arabnia, PhD General Chair, The 2004 International Multiconference in Computer Science and Computer Engineering (IMCSE2004) The University of Georgia Department of Computer Science 415 Graduate Studies Research Center Athens, Georgia 30602-7404, U.S.A. Tel: (706) 542-3480 Fax: (706) 542-2966 E-mail: hra at cs.uga.edu SUBMISSION OF PAPERS: Prospective authors are invited to submit three copies of their draft paper (about 5 pages - single space, font size of 10 to 12) to H. R. Arabnia by the due date (who may be forwarding the papers to respective conference chairs/committees). E-mail submissions in MS document or PDF formats are preferable (Fax submissions are also acceptable.) The length of the Camera-Ready papers (if accepted) will be limited to 7 (IEEE style) pages. Papers must not have been previously published or currently submitted for publication elsewhere. The first page of the draft paper should include: title of the paper, name, affiliation, postal address, E-mail address, telephone number, & Fax number for each author. The first page should also include the name of the author who will be presenting the paper (if accepted) & a maximum of 5 keywords. LOCATION OF CONFERENCES: The conferences will be held in the Monte Carlo Resort hotel, Las Vegas, Nevada, USA (with any overflows at other near-by hotels). The Monte Carlo Resort is a mega hotel with excellent conference facilities & over 3,000 rooms. The hotel is minutes from the airport with 24-hour shuttle service to & from the airport. This hotel has many recreational attractions, including: waterfalls, spa, pools & kiddie pools, sunning decks, Easy River water ride, wave pool with cascades, lighted tennis courts, health spa (with workout equipment, whirlpool, sauna, ...), arcade virtual reality game rooms, nightly shows, snack bars, a number of restaurants, shopping area, bars, ... Many of these attractions are open 24 hours a day & most are suitable for families & children. The negotiated room rate for conference attendees is very reasonable. The hotel is within walking distance from most other attractions (major shopping areas, recreational destinations, fine dining & night clubs, free street shows, ...). IMPORTANT DATES: Feb. 16, 2004: Draft papers (about 5 pages) due March 22, 2004: Notification of acceptance April 21, 2004: Camera-Ready papers & Prereg. due June 21-24, 2004: 2004 Int'l Multiconference in CS & CE Proposals to organize technical sessions should be submitted as soon as possible. PROPOSAL FOR ORGANIZING TECHNICAL SESSIONS: Each technical session will have at least 6 paper presentations (from different authors). The session chairs will be responsible for all aspects of their sessions; including, soliciting papers, reviewing, selecting, ... The names of session chairs will appear as Associate Editors in the conference proceedings. After the conference, some sessions will be considered for publication in appropriate journals as Special Issues with the session proposer as the Guest Editor of the journal. Proposals to organize technical sessions should include the following information: name and address (+ E-mail) of proposer, title of session, a 100-word description of the topic of the session, and a short description on how the session will be advertised (in most cases, session proposers solicit papers from colleagues and researchers whose work is known to the session proposer). Mail your proposal to H. R. Arabnia (address is given above); E-mail submissions are preferred. MEMBERS OF PROGRAM & ORGANIZING COMMITTEES: The Program Committee includes members of chapters of World Academy of Science (chapters: supercomputing; scientific computing; artificial intelligence; imaging science; databases; simulation; software engineering; embedded systems; internet and web technologies; communications; computer security; and bioinformatics.) The Program Committee for individual conferences is currently being formed. Those interested in joining the Program Committee should email H. R. Arabnia (hra at cs.uga.edu) the following information: Name, affiliation and position, complete mailing address, email address, tel/fax numbers, a short biography together with research interests and the name of the conference offering to help with. EXHIBITION: An exhibition is being planned. Interested parties should contact H. R. Arabnia (hra at cs.uga.edu). All exhibitors will be considered to be the co-sponsors of the conference. Topical scope for each conference can be found at http://www.world-academy-of-science.org From dmb at mrc-dunn.cam.ac.uk Sat Dec 6 08:50:01 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Sat, 6 Dec 2003 13:50:01 -0000 (GMT) Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: <3FD0D342.9050302@burnham.org> References: <3FD0D342.9050302@burnham.org> Message-ID: <33181.62.253.132.36.1070718601.squirrel@www.mrc-dunn.cam.ac.uk> Is a profile better at detecting homologues than each of its individual sequences? Is the whole more than the sum of its parts? This is generally the impression people have of profiles, but is it true? Cheers. Dan. ++ Iddo Friedberg-- > Slight correction: FFAS aligns a /profile/ against a profile database, not a > /sequence/ against a profile database. More sensitive that way. > > ./I > > > Rong Chen wrote: >> Hi, >> >> Normally, we align a profile against a sequence database in psi-blast. I heard >> that we could also cat all profiles to create a database, and align a sequence >> against this profile database. Did anyone hear anything about it? Is it a new >> program or a new option in psi-blast? >> >> Thank you. >> >> Rong >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> Rong Chen, Ph.D. >> Scientist >> Protein Engineering >> Accelrys Inc. >> San Diego, CA 92121 >> Tel: (858)799-5304(office) >> E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >> >> >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From mgollery at unr.edu Sat Dec 6 11:53:54 2003 From: mgollery at unr.edu (Martin Gollery) Date: Sat, 6 Dec 2003 08:53:54 -0800 Subject: [BiO BB] A question about profile database in psi-blast. In-Reply-To: <33181.62.253.132.36.1070718601.squirrel@www.mrc-dunn.cam.ac.uk> References: <3FD0D342.9050302@burnham.org> <33181.62.253.132.36.1070718601.squirrel@www.mrc-dunn.cam.ac.uk> Message-ID: <1070729634.3fd209a22b6db@webmail.unr.edu> Yes, it is. The reason is that searching with individual sequences relys on standard generic scoring matrices, which are based on substitution rates over an entire dataset. There is no information on importance of location in a PAM or Blosum matrix, which is a serious flaw- some locations in a protein cannot be substituted without changing the function of the protein. Other positions are not critical at all. Smith-Waterman, Fasta and BLASt searches do not know anything about position, and so do not consider this information. Marty Quoting Dan Bolser : > > Is a profile better at detecting homologues than each of its individual > sequences? > > Is the whole more than the sum of its parts? > > This is generally the impression people have of profiles, but is it true? > > Cheers. > Dan. > > ++ Iddo Friedberg-- > > Slight correction: FFAS aligns a /profile/ against a profile database, not > a > > /sequence/ against a profile database. More sensitive that way. > > > > ./I > > > > > > Rong Chen wrote: > >> Hi, > >> > >> Normally, we align a profile against a sequence database in psi-blast. I > heard > >> that we could also cat all profiles to create a database, and align a > sequence > >> against this profile database. Did anyone hear anything about it? Is it a > new > >> program or a new option in psi-blast? > >> > >> Thank you. > >> > >> Rong > >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >> Rong Chen, Ph.D. > >> Scientist > >> Protein Engineering > >> Accelrys Inc. > >> San Diego, CA 92121 > >> Tel: (858)799-5304(office) > >> E-mail: rong at zlab.bu.edu http://zlab.bu.edu/~rong > >> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >> > >> > >> _______________________________________________ > >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > >> > >> > > > > -- > > Iddo Friedberg, Ph.D. > > The Burnham Institute > > 10901 N. Torrey Pines Rd. > > La Jolla, CA 92037 > > USA > > Tel: +1 (858) 646 3100 x3516 > > Fax: +1 (858) 646 3171 > > http://ffas.ljcrf.edu/~iddo > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From mar_jaya at yahoo.co.in Fri Dec 5 23:59:20 2003 From: mar_jaya at yahoo.co.in (=?iso-8859-1?q?muthu=20kum?=) Date: Sat, 6 Dec 2003 04:59:20 +0000 (GMT) Subject: [BiO BB] project Message-ID: <20031206045920.700.qmail@web8106.mail.in.yahoo.com> Dear raj my name is muthu. I am studying in M.Sc bioinformatics. our college has no staff for bioinformatics. our college has no senior staff for bioinformatics. I choose three topics for my project work. 1.Drug design 2.homology modeling 3.comparative genomics. I have no idea about how to desing the drug using bioinformatics tools and other two topics how to work. I believe you only. Because I am coming from village. I have no staff, no senior for bioinformatics. so I expect your answer. don't forget my email. please kindly anser my doubt. my email:mar_jaya at yahoo.co.in Yahoo! India Mobile: Ringtones, Wallpapers, Picture Messages and more.Download now. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Natalio.Krasnogor at nottingham.ac.uk Tue Dec 9 09:57:11 2003 From: Natalio.Krasnogor at nottingham.ac.uk (Natalio Krasnogor) Date: Tue, 09 Dec 2003 14:57:11 +0000 Subject: [BiO BB] About the Bioinformatics survey Message-ID: <3FD5E2C7.EFC7A42F@nottingham.ac.uk> Dear Colleagues, Thanks for you responses so far to my webioner ( http://www.cs.nott.ac.uk/~nxk/POLL2/natWebioner.html ) As a clarification I wanted to point out that: - by default all the answers I receive will be deemed anonymous (even if you input your personal details). If I need to cite (part of) your answers I will first ask for your permision to do so. - after I close the webioner and I collect my findings I will make available the results. thanks again for your time. Nat -- ---------------------------------------------------------------------------------------- NATALIO KRASNOGOR, Ph.D. Automated Scheduling, Planning and Optimisation Group Lecturer School of Computer Sciences and Information Technology Jubilee Campus University of Nottingham Tel.: +44 - 0115 - 8467592 Nottingham, NG82BB United Kingdom URL: http://www.cs.nott.ac.uk/~nxk/ e-mail: Natalio.Krasnogor at nottingham.ac.uk ---------------------------------------------------------------------------------------- From idoerg at burnham.org Tue Dec 9 12:46:36 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Tue, 09 Dec 2003 09:46:36 -0800 Subject: [BiO BB] About the Bioinformatics survey In-Reply-To: <3FD5E2C7.EFC7A42F@nottingham.ac.uk> References: <3FD5E2C7.EFC7A42F@nottingham.ac.uk> Message-ID: <3FD60A7C.6000404@burnham.org> Nat, Q2: is 10 the highest ranking or the lowest-ranking option? Iddo Natalio Krasnogor wrote: > Dear Colleagues, > > Thanks for you responses so far to my webioner ( > http://www.cs.nott.ac.uk/~nxk/POLL2/natWebioner.html ) > As a clarification I wanted to point out that: > > - by default all the answers I receive > will be deemed anonymous (even if you input your personal details). > If I need to cite (part of) your answers I will first ask for your > permision to do so. > > - after I close the webioner and I collect my findings I will make > available the results. > > > thanks again for your time. > > Nat -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From sjung at CLEMSON.EDU Wed Dec 10 15:21:28 2003 From: sjung at CLEMSON.EDU (Sook Jung) Date: Wed, 10 Dec 2003 15:21:28 -0500 (EST) Subject: [BiO BB] Seeking project for a high school student Message-ID: <4845.155.138.25.52.1071087688.squirrel@mail.clemson.edu> Dear all, Can anybody suggest potential bioinformatics projects for a high school student for science? He is a bright student -especially good at biology, chemistry and mathmatics- but not a lot of programming experience (some visual basic). Thank you. From idoerg at burnham.org Wed Dec 10 15:33:11 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 10 Dec 2003 12:33:11 -0800 Subject: [BiO BB] Seeking project for a high school student In-Reply-To: <4845.155.138.25.52.1071087688.squirrel@mail.clemson.edu> References: <4845.155.138.25.52.1071087688.squirrel@mail.clemson.edu> Message-ID: <3FD78307.4090000@burnham.org> How about a protein sequence colorer? Read a FASTA file, and use different color schemes based on charge, hydrophobicity, size, polarity. This could also be turned into a simple hydropathy indexing plot, thus a primitive membrane protein predictor. If this sounds like an underkill, apply same idea to a multiple sequence alignment. Conservation indices etc. may be calculated for each column. (For a given alignment of course, writing a mutliple sequence aligner from scratch is definitely *not* a school project :) This would teach: 1) Simple parsing 2) a lot of protein biochemistry 3) If the secind option is taken, a bit of information theory. ./I Sook Jung wrote: > Dear all, > > Can anybody suggest potential bioinformatics projects for a high school > student for science? He is a bright student -especially good at biology, > chemistry and mathmatics- but not a lot of programming experience (some > visual basic). > Thank you. > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From jordanmswanson at yahoo.com Thu Dec 11 18:44:15 2003 From: jordanmswanson at yahoo.com (jordan swanson) Date: Thu, 11 Dec 2003 15:44:15 -0800 (PST) Subject: [BiO BB] Is it possible to Blast against genBank files Message-ID: <20031211234415.57591.qmail@web41906.mail.yahoo.com> I've downloaded and installed blast and some FASTA databases for a lab I'm working for. I have a user who is blasting (using blastx) against a list of clones. Unfortunately, the database files I downloaded do not contain enough information for her(because they are fasta format) This leads me to believe that I need a local copy of the genBank files. I've downloaded gbpln[1-9].seq from NCBI. (we only need plant files). Is it possible to blast against these gb files? Also, what options do I need to use on formatdb to create the correct index files? If my questions are out of place here, let me know and I'll desist. -Jordan M Swanson __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ From idoerg at burnham.org Thu Dec 11 18:57:46 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 11 Dec 2003 15:57:46 -0800 Subject: [BiO BB] Is it possible to Blast against genBank files In-Reply-To: <20031211234415.57591.qmail@web41906.mail.yahoo.com> References: <20031211234415.57591.qmail@web41906.mail.yahoo.com> Message-ID: <3FD9047A.2090201@burnham.org> jordan swanson wrote: > I've downloaded and installed blast and some FASTA > databases for a lab I'm working for. I have a user > who is blasting (using blastx) against a list of > clones. Unfortunately, the database files I > downloaded do not contain enough information for > her(because they are fasta format) You mean that the BLAST results only have the Fasta file annotation in them. Well, AFAIK, the only input to formatdb is Fasta or ASN.1. The output, anyhow, would be a one-liner. How about giving her the output in HTML (-T option)? blast automatically builds a link from each hit to the NCBI page. So using a browser, your coworker can skim the one-line annotation, and then click & delve into the more interesting ones. > > This leads me to believe that I need a local copy of > the genBank files. I've downloaded gbpln[1-9].seq > from NCBI. (we only need plant files). Is it possible > to blast against these gb files? Also, what options > do I need to use on formatdb to create the correct > index files? > You can only formatdb from ASN.1 or Fasta formats. > If my questions are out of place here, let me know and > I'll desist. > > -Jordan M Swanson > > __________________________________ > Do you Yahoo!? > New Yahoo! Photos - easier uploading and sharing. > http://photos.yahoo.com/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From johnkecops at yahoo.co.uk Thu Dec 11 21:45:56 2003 From: johnkecops at yahoo.co.uk (=?iso-8859-1?q?John=20Kecops=20Kleinsteuber?=) Date: Fri, 12 Dec 2003 02:45:56 +0000 (GMT) Subject: [BiO BB] xylitol enzyme Message-ID: <20031212024556.26145.qmail@web25005.mail.ukl.yahoo.com> Hi, I'm a student of Chemistry in University of Indonesia. Currently, I'm working my research about xylitol enzyme. I want to study its hidrolisis yield on rice beech. The problem is: I have trouble on many aspects. I don't know how to prepare the sample, and I don't know how to caracterize it result with HPLC. Is any one can help me? Please sent me your e-mail to me if you can help me with this xylitol enzyme. Thank you. --------------------------------- BT Yahoo! Broadband - Save ?80 when you order online today. Hurry! Offer ends 21st December 2003. The way the internet was meant to be. -------------- next part -------------- An HTML attachment was scrubbed... URL: From derek at biotechrecruiter.org Fri Dec 12 10:41:53 2003 From: derek at biotechrecruiter.org (Derek Pyper) Date: Fri, 12 Dec 2003 07:41:53 -0800 Subject: [BiO BB] remove In-Reply-To: <1758.172.16.8.66.1070642029.squirrel@cdl.msitprogram.net> Message-ID: Derek Pyper Biotech Recruiters International, Inc. Principal Office 916-652-2186 Fax 916-652-2178 Email: Derek at biotech-recruiters.com URL: www.biotech-recruiters.com CONFIDENTIALITY STATEMENT: This electronic message contains privileged and confidential information from Biotech Recruiters International, Inc. This information is intended solely for the use of the individual(s) or entity(ies) named above. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of the contents of this message is prohibited. If you have received this email in error, please notify us immediately by telephone at 916-652-2186 or by email reply. Thank you. -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Radhika Tallamraju Sent: Friday, December 05, 2003 8:34 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] help regarding MEME program Can anyone suggest me how to construct log odds matrix for a given consensus sequence. I need this to run MAST program. Regards, Radhika. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- A non-text attachment was scrubbed... Name: Derek Pyper (derek at biotech-recruiters.com).vcf Type: text/x-vcard Size: 537 bytes Desc: not available URL: From tfiedler at rsmas.miami.edu Fri Dec 12 23:22:43 2003 From: tfiedler at rsmas.miami.edu (Tristan Fiedler) Date: Fri, 12 Dec 2003 23:22:43 -0500 (EST) Subject: [BiO BB] cDNA Library Subtraction - Bioinformatics In-Reply-To: <20031213000321.13084.qmail@web41208.mail.yahoo.com> References: <20031213000321.13084.qmail@web41208.mail.yahoo.com> Message-ID: <50125.129.171.111.149.1071289363.squirrel@domino.rsmas.miami.edu> Using the current state of the art bioinformatics tools/software, what is the preferred method of *identifying EST sequences* for the subtraction procedure of a cDNA library ? In order to decrease the abundant messages which dominate cDNA libraries, I hope to identify the longest, most abundant, and annotatable (based on e.g. swissprot) ESTs. I would like to get expert opinions on how to most effectively go about it. I have several thousand ESTs and would, for at least this first round, like to identify 96 clones which are the most abundant/longest/annotatable. Approaches I have considered are : 1. Running the entire dataset through CAP3 to produce contigs. Then take the consensus sequence for each contig and run a blastp against swissprot to see if is annotatable. 2. Running an all against all blast search using the ESTs as both the query and the database. Additionally, one could make the database a combination of both the ESTs and swissprot, thus indicating not only which sequences have similar/identical matches within the EST database, but also whether they have a homolog in swissprot Does anything exist in bioperl which performs the necessary sequence analysis for subtraction of a cDNA library? BTW, if these are not the correct listserv/bulletin boards for such a query, please let me know the preferred location. Thank you and Happy Holidays! Tristan Fiedler -- Tristan J. Fiedler, Ph.D. Postdoctoral Research Fellow - Walsh Laboratory NIEHS Marine & Freshwater Biomedical Sciences Center Rosenstiel School of Marine & Atmospheric Sciences University of Miami tfiedler at rsmas.miami.edu t.fiedler at umiami.edu (alias) 305-361-4626 From cdwan at mail.ahc.umn.edu Sat Dec 13 17:27:16 2003 From: cdwan at mail.ahc.umn.edu (Chris Dwan (CCGB)) Date: Sat, 13 Dec 2003 16:27:16 -0600 (CST) Subject: [BiO BB] cDNA Library Subtraction - Bioinformatics In-Reply-To: <50125.129.171.111.149.1071289363.squirrel@domino.rsmas.miami.edu> References: <20031213000321.13084.qmail@web41208.mail.yahoo.com> <50125.129.171.111.149.1071289363.squirrel@domino.rsmas.miami.edu> Message-ID: > Using the current state of the art bioinformatics tools/software, what is > the preferred method of *identifying EST sequences* for the subtraction > procedure of a cDNA library ? This is an interesting question to me, since the answer is so clearly a protocol combining a variety of existing tools rather than a single general tool. BioPerl is an excellent framework for scripting such protocols. > In order to decrease the abundant messages which dominate cDNA libraries, > I hope to identify the longest, most abundant, and annotatable (based on > e.g. swissprot) ESTs. I would like to get expert opinions on how to most > effectively go about it. I have several thousand ESTs and would, for at > least this first round, like to identify 96 clones which are the most > abundant/longest/annotatable. We have a pipeline to perform almost exactly the opposite analysis (find novel genes with no obvious homologs), some parts of which might be useful to you: 1) Perform quality analysis on each EST - Trim low quality reads from both ends until the sequence is at most K percent ambiguous bases. K varies depending on the experiment. - Look for the primer / linker site at each end of the sequence and remove it if found. Leaving these in makes for *great* anchors for spurious assemblies of contigs. - BLAST against E. Coli as well as popular phage sequences to look for obvious contamination. - BLAST against the human chromosomes to look for contamination 2) Assemble contigs - We use phrap, mostly because we have some expertise with it. There are other options available. My opinion is that it's better to use a tool that is well understood at your lab than to try to learn an unknown that may or may not be better. 3) (optional) go through the contigs and break up those that do not have good support across their entire length. This is currently a real pain, but hopefully we'll have an automated system trained "real soon now." 4) BLASTX contigs vs PIR-NREF (again, a local favorite). Anything that can be annotated this way, remove from further steps 5) TBLASTX contigs vs. NCBI NT. 6) Further manual analysis using HMMER and other tools. > Does anything exist in bioperl which performs the necessary sequence > analysis for subtraction of a cDNA library? All of these piece-parts can be scripted using BioPerl, but I'm not aware of any single general tool that does exactly what you're looking for. I am very interested to hear about how other shops do their EST analysis these days. -Chris Dwan University of Minnesota From gilbertd at bio.indiana.edu Sun Dec 14 12:38:47 2003 From: gilbertd at bio.indiana.edu (Don Gilbert) Date: Sun, 14 Dec 2003 12:38:47 -0500 (EST) Subject: [BiO BB] Biology software reviews for Brief. in Bioinformatics Message-ID: <200312141738.hBEHclM14000@cricket.bio.indiana.edu> The journal Briefings in Bioinformatics is seeking reviews of bioinformatics software. If you have a favorite program, or have compared two or more programs and would like to write about their benefits and drawbacks, please contact me. The target audience includes a range of biologists and bioinformaticians, from academia, goverment and industry. A review should be about practical aspects of the software, and be helpful to this range of readers. One caveat is that reviewers should not have associations with the software reviewed, and approach it impartially. Also suggestions for software to be reviewed are welcome. See more at http://www.henrystewart.com/journals/bib/ http://marmot.bio.indiana.edu/bibsoft/ -- software reviews Don Gilbert, software editor, BiB. gilbertd at indiana.edu bioinformatics, biology dept., indiana university, bloomington, in 47405 USA From venkata.satagopam at lionbioscience.com Mon Dec 15 05:19:34 2003 From: venkata.satagopam at lionbioscience.com (Venkata Satagopam) Date: Mon, 15 Dec 2003 11:19:34 +0100 Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #584 - 4 msgs Message-ID: <200312151020.hBFAKKb01593@admin05.lion-ag.de> Hello Jordan, Yes, it is possible, but first you have to create a Fasta file out of these Genbank files gbpln[1-9].seq. So that means you have to extract all the sequences from above files and store them in a FASTA format. Once you have fasta file, then you have to create blastble by using formatdb by using following command formatdb -i -p F then you are able to blast against this fastafile. I hope this will help you, if you need more info please contact me either in the group or @ satagopam_p at yahoo.com regards venkata -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org]On Behalf Of bio_bulletin_board-request at bioinformatics.org Sent: Friday, December 12, 2003 6:01 PM To: bio_bulletin_board at bioinformatics.org Subject: BiO_Bulletin_Board digest, Vol 1 #584 - 4 msgs When replying, PLEASE edit your Subject line so it is more specific than "Re: BiO_Bulletin_Board digest, Vol..." Today's Topics: 1. Is it possible to Blast against genBank files (jordan swanson) 2. Re: Is it possible to Blast against genBank files (Iddo Friedberg) 3. xylitol enzyme (=?iso-8859-1?q?John=20Kecops=20Kleinsteuber?=) 4. remove (Derek Pyper) --__--__-- Message: 1 Date: Thu, 11 Dec 2003 15:44:15 -0800 (PST) From: jordan swanson To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Is it possible to Blast against genBank files Reply-To: bio_bulletin_board at bioinformatics.org I've downloaded and installed blast and some FASTA databases for a lab I'm working for. I have a user who is blasting (using blastx) against a list of clones. Unfortunately, the database files I downloaded do not contain enough information for her(because they are fasta format) This leads me to believe that I need a local copy of the genBank files. I've downloaded gbpln[1-9].seq from NCBI. (we only need plant files). Is it possible to blast against these gb files? Also, what options do I need to use on formatdb to create the correct index files? If my questions are out of place here, let me know and I'll desist. -Jordan M Swanson __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ --__--__-- Message: 2 Date: Thu, 11 Dec 2003 15:57:46 -0800 From: Iddo Friedberg To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Is it possible to Blast against genBank files Reply-To: bio_bulletin_board at bioinformatics.org jordan swanson wrote: > I've downloaded and installed blast and some FASTA > databases for a lab I'm working for. I have a user > who is blasting (using blastx) against a list of > clones. Unfortunately, the database files I > downloaded do not contain enough information for > her(because they are fasta format) You mean that the BLAST results only have the Fasta file annotation in them. Well, AFAIK, the only input to formatdb is Fasta or ASN.1. The output, anyhow, would be a one-liner. How about giving her the output in HTML (-T option)? blast automatically builds a link from each hit to the NCBI page. So using a browser, your coworker can skim the one-line annotation, and then click & delve into the more interesting ones. > > This leads me to believe that I need a local copy of > the genBank files. I've downloaded gbpln[1-9].seq > from NCBI. (we only need plant files). Is it possible > to blast against these gb files? Also, what options > do I need to use on formatdb to create the correct > index files? > You can only formatdb from ASN.1 or Fasta formats. > If my questions are out of place here, let me know and > I'll desist. > > -Jordan M Swanson > > __________________________________ > Do you Yahoo!? > New Yahoo! Photos - easier uploading and sharing. > http://photos.yahoo.com/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo --__--__-- Message: 3 Date: Fri, 12 Dec 2003 02:45:56 +0000 (GMT) From: =?iso-8859-1?q?John=20Kecops=20Kleinsteuber?= To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] xylitol enzyme Reply-To: bio_bulletin_board at bioinformatics.org --0-814827070-1071197156=:24403 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, I'm a student of Chemistry in University of Indonesia. Currently, I'm working my research about xylitol enzyme. I want to study its hidrolisis yield on rice beech. The problem is: I have trouble on many aspects. I don't know how to prepare the sample, and I don't know how to caracterize it result with HPLC. Is any one can help me? Please sent me your e-mail to me if you can help me with this xylitol enzyme. Thank you. --------------------------------- BT Yahoo! Broadband - Save ?80 when you order online today. Hurry! Offer ends 21st December 2003. The way the internet was meant to be. --0-814827070-1071197156=:24403 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
 Hi, I'm a student of Chemistry in University of Indonesia. Currently, I'm working my research about xylitol enzyme. I want to study its hidrolisis yield on rice beech. The problem is: I have trouble on many aspects. I don't know how to prepare the sample, and I don't know how to caracterize it result with HPLC. Is any one can help me? Please sent me your e-mail to me if you can help me with this xylitol enzyme. Thank you.

BT Yahoo! Broadband - Save ?80 when you order online today. Hurry! Offer ends 21st December 2003. The way the internet was meant to be. --0-814827070-1071197156=:24403-- --__--__-- Message: 4 Date: Fri, 12 Dec 2003 07:41:53 -0800 From: Derek Pyper To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] remove Reply-To: bio_bulletin_board at bioinformatics.org This is a multi-part message in MIME format. --Boundary_(ID_OeDcmc5TrzzOjm+W1FQqFg) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT Derek Pyper Biotech Recruiters International, Inc. Principal Office 916-652-2186 Fax 916-652-2178 Email: Derek at biotech-recruiters.com URL: www.biotech-recruiters.com CONFIDENTIALITY STATEMENT: This electronic message contains privileged and confidential information from Biotech Recruiters International, Inc. This information is intended solely for the use of the individual(s) or entity(ies) named above. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of the contents of this message is prohibited. If you have received this email in error, please notify us immediately by telephone at 916-652-2186 or by email reply. Thank you. -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Radhika Tallamraju Sent: Friday, December 05, 2003 8:34 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] help regarding MEME program Can anyone suggest me how to construct log odds matrix for a given consensus sequence. I need this to run MAST program. Regards, Radhika. _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board --Boundary_(ID_OeDcmc5TrzzOjm+W1FQqFg) Content-type: text/x-vcard; name="Derek Pyper (derek at biotech-recruiters.com).vcf" Content-transfer-encoding: 7BIT Content-disposition: attachment; filename="Derek Pyper (derek at biotech-recruiters.com).vcf" BEGIN:VCARD VERSION:2.1 N:Pyper;Derek FN:Derek Pyper (derek at biotech-recruiters.com) ORG:Biotech Recruiters International TITLE:Principal TEL;WORK;VOICE:(916) 652-2186 TEL;CELL;VOICE:(415) 531-2507 TEL;WORK;FAX:(916) 652-2178 ADR;WORK:;;8515 Nob Hill Lane;Granite Bay;Ca;95746;United States of America LABEL;WORK;ENCODING=QUOTED-PRINTABLE:8515 Nob Hill Lane=0D=0AGranite Bay, Ca 95746=0D=0AUnited States of America URL;WORK:http://www.biotech-recruiters.com EMAIL;PREF;INTERNET:derek at biotech-recruiters.com REV:20031208T150339Z END:VCARD --Boundary_(ID_OeDcmc5TrzzOjm+W1FQqFg)-- --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest --- Venkata Pardhasaradhi Satagopam, Bioinformatics Scientist, Genomics IT Research, Office Address :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414 Home Address :Fritz-Frey-Str.8/112.301.01, 69121 Heidelberg, GERMANY. Tel:0049-(0)6221 729667 (Mobile):0049-(0)179 7927494 From tsucheta at hotmail.com Mon Dec 15 06:29:39 2003 From: tsucheta at hotmail.com (Sucheta Tripathi) Date: Mon, 15 Dec 2003 11:29:39 +0000 Subject: [BiO BB] RE: BiO_Bulletin_Board digest, Vol 1 #586 - 1 msg Message-ID: Hi, I think there are several ways one can do ESt analysis if you have large number of sequences. I am not sure if your sequences have been quality trimmed, and cleaned of vector, primer sequences. The next step would be to clusetr them followed by assembly. There are lots of tools available, and many people develop their own, as we have with d2cluster and cap3. Alternatively you can obtain a copy of tgicl developed by TIGR. It is quite handy and does both clustering and assembly. The clustering is based on megablast and assembly on cap3. For running a blast, you can get blast help from its ftp site, and can setup local blast and run blast for all the sequences at a time. You can't run blast against swissprot and EST sequences at one go. since you can't format data for protein and nucleotide sequences together. Hope this helps Sucheta 
**********************************************
Sucheta Tripathy, 
Ph.D.                   
                        
Senior Research 
Associate,                
                        
Virginia Bioinformatics 
Institute,        
Virginia 
Polytechnic & State Institute,   
Virginia, USA, 
24061                      

Phone 
540-231-8138(O)                     

          
540-443-1763(H) 
>From: bio_bulletin_board-request at bioinformatics.org >Reply-To: bio_bulletin_board at bioinformatics.org >To: bio_bulletin_board at bioinformatics.org >Subject: BiO_Bulletin_Board digest, Vol 1 #586 - 1 msg >Date: Sun, 14 Dec 2003 12:01:10 -0500 (EST) > >When replying, PLEASE edit your Subject line so it is more specific >than "Re: BiO_Bulletin_Board digest, Vol..." > > >Today's Topics: > > 1. Re: cDNA Library Subtraction - Bioinformatics (Chris Dwan (CCGB)) > >--__--__-- > >Message: 1 >Date: Sat, 13 Dec 2003 16:27:16 -0600 (CST) >From: "Chris Dwan (CCGB)" >To: bio_bulletin_board at bioinformatics.org >Cc: t.fiedler at umiami.edu >Subject: Re: [BiO BB] cDNA Library Subtraction - Bioinformatics >Reply-To: bio_bulletin_board at bioinformatics.org > > > > Using the current state of the art bioinformatics tools/software, what >is > > the preferred method of *identifying EST sequences* for the subtraction > > procedure of a cDNA library ? > >This is an interesting question to me, since the answer is so clearly a >protocol combining a variety of existing tools rather than a single >general tool. BioPerl is an excellent framework for scripting such >protocols. > > > In order to decrease the abundant messages which dominate cDNA >libraries, > > I hope to identify the longest, most abundant, and annotatable (based on > > e.g. swissprot) ESTs. I would like to get expert opinions on how to >most > > effectively go about it. I have several thousand ESTs and would, for at > > least this first round, like to identify 96 clones which are the most > > abundant/longest/annotatable. > >We have a pipeline to perform almost exactly the opposite analysis (find >novel genes with no obvious homologs), some parts of which might be >useful to you: > >1) Perform quality analysis on each EST > - Trim low quality reads from both ends until the sequence is > at most K percent ambiguous bases. K varies depending on the > experiment. > - Look for the primer / linker site at each end of the sequence and > remove it if found. Leaving these in makes for *great* > anchors for spurious assemblies of contigs. > - BLAST against E. Coli as well as popular phage sequences to look for > obvious contamination. > - BLAST against the human chromosomes to look for contamination > >2) Assemble contigs > - We use phrap, mostly because we have some expertise with it. > There are other options available. My opinion is that it's better > to use a tool that is well understood at your lab than to try to > learn an unknown that may or may not be better. > >3) (optional) go through the contigs and break up those that do > not have good support across their entire length. This is currently > a real pain, but hopefully we'll have an automated system trained > "real soon now." > >4) BLASTX contigs vs PIR-NREF (again, a local favorite). Anything that > can be annotated this way, remove from further steps > >5) TBLASTX contigs vs. NCBI NT. > >6) Further manual analysis using HMMER and other tools. > > > Does anything exist in bioperl which performs the necessary sequence > > analysis for subtraction of a cDNA library? > >All of these piece-parts can be scripted using BioPerl, but I'm not aware >of any single general tool that does exactly what you're looking for. > >I am very interested to hear about how other shops do their EST analysis >these days. > >-Chris Dwan > University of Minnesota > > >--__--__-- > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > >End of BiO_Bulletin_Board Digest _________________________________________________________________ Contact brides & grooms FREE! Only on www.shaadi.com. http://www.shaadi.com/ptnr.php?ptnr=hmltag Register now! From westerman at purdue.edu Mon Dec 15 17:15:37 2003 From: westerman at purdue.edu (Rick Westerman) Date: Mon, 15 Dec 2003 17:15:37 -0500 Subject: [BiO BB] Re: EST clustering In-Reply-To: <20031214170112.245A2D29B1@www.bioinformatics.org> Message-ID: <5.1.0.14.2.20031215171210.02c65da0@westerm.mail.purdue.edu> Chris Dwan asks: >I am very interested to hear about how other shops do their EST analysis >these days. For the following two steps we use the 'stackpack' program from Electric Genetics >2) Assemble contigs > - We use phrap, mostly because we have some expertise with it. > There are other options available. My opinion is that it's better > to use a tool that is well understood at your lab than to try to > learn an unknown that may or may not be better. > >3) (optional) go through the contigs and break up those that do > not have good support across their entire length. This is currently > a real pain, but hopefully we'll have an automated system trained > "real soon now." Annotation and other post-EST assembly steps are project dependent. Blast and HAMMER certainly play a role here. -- Rick Rick Westerman westerman at purdue.edu Phone: (765) 494-0505 FAX: (765) 496-7255 Department of Horticulture and Landscape Architecture 625 Agriculture Mall Drive West Lafayette, IN 47907-2010 Physically located in room S049, WSLR building Bioinformatics specialist at the Genomics Facility. href="http://www.genomics.purdue.edu/~westerm" From tibs at stat.Stanford.EDU Mon Dec 15 19:00:57 2003 From: tibs at stat.Stanford.EDU (Rob Tibshirani) Date: Mon, 15 Dec 2003 16:00:57 -0800 Subject: [BiO BB] (no subject) Message-ID: <200312160000.hBG00vsP023400@miller.Stanford.EDU> Data mining and bioinformatics short course: Palo Alto Short course: Statistical Learning and Data Mining Trevor Hastie and Robert Tibshirani, Stanford University Sheraton Hotel Palo Alto, CA Feb 26-27, 2004 This two-day course gives a detailed overview of statistical models for data mining, inference and prediction. With the rapid developments in internet technology, genomics and other high-tech industries, we rely increasingly more on data analysis and statistical models to exploit the vast amounts of data at our fingertips. This sequel to our popular "Modern Regression and Classification" course covers many new areas of unsupervised learning and data mining, and gives an in-depth treatment of some of the hottest tools in supervised learning. The first course is not a prerequisite for this new course. Day one focuses on state-of-art methods for supervised learning, including PRIM, boosting, support vector machines, and very recent work on least angle regression and the lasso. Day two covers unsupervised learning, including clustering, principal components, principal curves and self-organizing maps. Many applications will be discussed, including the analysis of DNA expression arrays - one of the hottest new areas in biology! ################################################### Much of the material is based on the best selling book: Elements of Statistical Learning: data mining, inference and prediction Hastie, Tibshirani & Friedman, Springer-Verlag, 2001 http://www-stat.stanford.edu/ElemStatLearn/ A copy of this book will be given to all attendees. ################################################### Go to the site http://www-stat.stanford.edu/~hastie/mrc.html for more information and online registration. From john_abraham_bio at yahoo.com Wed Dec 17 06:19:41 2003 From: john_abraham_bio at yahoo.com (John Abraham) Date: Wed, 17 Dec 2003 03:19:41 -0800 (PST) Subject: [BiO BB] universal primer Message-ID: <20031217111941.4691.qmail@web60804.mail.yahoo.com> Hi All I am new to this biobulletin and really dont know whether this is a correct forum to post my query I am basically looking for desiging universal primers for a gene that is conserved across eukaryotes and prokaryotes (like 5s rRNA),using which I want to detect source of my host cell DNA contaminansts from which my protein of interest is extracted. Kindly help me in this query Thanks in advances John --------------------------------- Do you Yahoo!? Free Pop-Up Blocker - Get it now -------------- next part -------------- An HTML attachment was scrubbed... URL: From rajat at isical.ac.in Wed Dec 17 07:52:46 2003 From: rajat at isical.ac.in (Rajat Kumar De) Date: Wed, 17 Dec 2003 18:22:46 +0530 Subject: [BiO BB] request for suggestion References: <20031217111941.4691.qmail@web60804.mail.yahoo.com> Message-ID: <3FE0519E.6B6E1B41@isical.ac.in> Dear Colleague, I am looking for some papers on the mathematical modeling of following controlling factors of gene expression. It would be a great help to me, if somebody can provide me some papers/links or some suggestions, on the mathematical models of these factors in controlling gene expression. The controlling factors are: 1. Chromatin Structure 2. Transcriptional Initiation 3. Transcript Processing and Modification 4. RNA Transport 5. Transcript Stability 6. Translational Initiation 7. Post-Translational Modification 8. Protein Transport 9. Control of Protein Stability Please also let me know, if there are other controlling factors of gene expression. Regards, Rajat ****************************************************************** * Rajat K. De, Ph.D. | Telephone * * Assistant Professor | Office : 91-33-25753105 * * Machine Intelligence Unit | Residence : 91-33-25796860 * * Indian Statistical Institute | Mobile : 91-9830013571 * * 203 B.T. Road | Fax : 91-33-25783357 * * Kolkata 700108 | 91-33-25773035 * * INDIA. | Email : rajat at isical.ac.in * ****************************************************************** From munniss1 at yahoo.co.in Wed Dec 17 03:40:01 2003 From: munniss1 at yahoo.co.in (=?iso-8859-1?q?vodnala=20munender?=) Date: Wed, 17 Dec 2003 08:40:01 +0000 (GMT) Subject: [BiO BB] sir Message-ID: <20031217084001.84690.qmail@web8207.mail.in.yahoo.com> good morning sir sir i am student life sciences,sir i very much interested in doing phd in sweedon , sir plz can u provide all information about phd programm in sweedon sir what are the qualifications and how to apply thanking u sir vodnala munender MSc microbiology Osmania university andhrapradesh india email: munniss1 at yahoo.co.in Yahoo! India Mobile: Ringtones, Wallpapers, Picture Messages and more.Download now. -------------- next part -------------- An HTML attachment was scrubbed... URL: From ispeaks at bellsouth.net Wed Dec 17 09:42:33 2003 From: ispeaks at bellsouth.net (irene) Date: Wed, 17 Dec 2003 06:42:33 -0800 Subject: [BiO BB] info. Message-ID: <000a01c3c4ac$02fd9ca0$bd292343@HPAuthorizedCustomer> I need the name for chemical L-12-6, 590, 997, TPM, and where to purchase them, and what is biocide -------------- next part -------------- An HTML attachment was scrubbed... URL: From jordanmswanson at yahoo.com Thu Dec 18 15:53:51 2003 From: jordanmswanson at yahoo.com (jordan swanson) Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST) Subject: [BiO BB] Is it possible to Blast against genBank files In-Reply-To: <3FD9047A.2090201@burnham.org> Message-ID: <20031218205351.12652.qmail@web41901.mail.yahoo.com> > You mean that the BLAST results only have the Fasta > file annotation in > them. Well, AFAIK, the only input to formatdb is > Fasta or ASN.1. The > output, anyhow, would be a one-liner. > > How about giving her the output in HTML (-T option)? > blast automatically > builds a link from each hit to the NCBI page. So > using a browser, your > coworker can skim the one-line annotation, and then > click & delve into > the more interesting ones. We did try that, however with the large number of sequences she needed to look up, she was black-listed from their machine. We need to find the full GenBank entry given a particular identifier, unfortunately the easiest way I've found so far seems to be the Entrez system, and that appears to not be possible to download. Is there another way to get the full genbank entry given the identifier? --- Jordan Swanson __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ From idoerg at burnham.org Thu Dec 18 16:00:25 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Thu, 18 Dec 2003 13:00:25 -0800 Subject: [BiO BB] Is it possible to Blast against genBank files In-Reply-To: <20031218205351.12652.qmail@web41901.mail.yahoo.com> References: <20031218205351.12652.qmail@web41901.mail.yahoo.com> Message-ID: <3FE21569.3090706@burnham.org> Biopython has something that can do that. Maybe Bioperl too. Let me know if you want the Python code. ./I jordan swanson wrote: >>You mean that the BLAST results only have the Fasta >>file annotation in >>them. Well, AFAIK, the only input to formatdb is >>Fasta or ASN.1. The >>output, anyhow, would be a one-liner. >> >>How about giving her the output in HTML (-T option)? >>blast automatically >>builds a link from each hit to the NCBI page. So >>using a browser, your >>coworker can skim the one-line annotation, and then >>click & delve into >>the more interesting ones. > > > We did try that, however with the large number of > sequences she needed to look up, she was black-listed > from their machine. We need to find the full GenBank > entry given a particular identifier, unfortunately the > easiest way I've found so far seems to be the Entrez > system, and that appears to not be possible to > download. Is there another way to get the full > genbank entry given the identifier? > > --- > Jordan Swanson > > __________________________________ > Do you Yahoo!? > New Yahoo! Photos - easier uploading and sharing. > http://photos.yahoo.com/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo From boris.steipe at utoronto.ca Thu Dec 18 17:01:20 2003 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu, 18 Dec 2003 17:01:20 -0500 Subject: [BiO BB] Is it possible to Blast against genBank files References: <20031218205351.12652.qmail@web41901.mail.yahoo.com> Message-ID: <3FE223AF.C9B252B7@utoronto.ca> jordan swanson wrote: > > > You mean that the BLAST results only have the Fasta > > file annotation in > > them. Well, AFAIK, the only input to formatdb is > > Fasta or ASN.1. The > > output, anyhow, would be a one-liner. > > > > How about giving her the output in HTML (-T option)? > > blast automatically > > builds a link from each hit to the NCBI page. So > > using a browser, your > > coworker can skim the one-line annotation, and then > > click & delve into > > the more interesting ones. > > We did try that, however with the large number of > sequences she needed to look up, she was black-listed > from their machine. We need to find the full GenBank > entry given a particular identifier, unfortunately the > easiest way I've found so far seems to be the Entrez > system, and that appears to not be possible to > download. Is there another way to get the full > genbank entry given the identifier? > > --- > Jordan Swanson Yes, you can get the files through the SeqHound remote Perl API - easy to program and no blacklists. See: and especially: Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe From venkata.satagopam at lionbioscience.com Fri Dec 19 12:55:28 2003 From: venkata.satagopam at lionbioscience.com (Venkata Satagopam) Date: Fri, 19 Dec 2003 18:55:28 +0100 Subject: [BiO BB] RE: Message-ID: <200312191756.hBJHuMa10990@admin05.lion-ag.de> Yes, you can get the full entry of GenBank from any public SRS servers. Here is the link where you can found many public SRS servers.. http://www.lionbio.co.uk/publicsrs.html OR you can look at http://igbmc.u-strasbg.fr/srs6/ regards venkata -----Original Message----- From: Posted At: Tuesday, January 01, 1991 1:00 AM Posted To: Inbox Conversation: Subject: When replying, PLEASE edit your Subject line so it is more specific than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any unrelated text from the body. Today's Topics: 1. Re: Is it possible to Blast against genBank files (jordan swanson) 2. Re: Is it possible to Blast against genBank files (Iddo Friedberg) 3. Re: Is it possible to Blast against genBank files (Boris Steipe) --__--__-- Message: 1 Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST) From: jordan swanson Subject: Re: [BiO BB] Is it possible to Blast against genBank files To: bio_bulletin_board at bioinformatics.org Reply-To: bio_bulletin_board at bioinformatics.org > You mean that the BLAST results only have the Fasta > file annotation in > them. Well, AFAIK, the only input to formatdb is > Fasta or ASN.1. The > output, anyhow, would be a one-liner. > > How about giving her the output in HTML (-T option)? > blast automatically > builds a link from each hit to the NCBI page. So > using a browser, your > coworker can skim the one-line annotation, and then > click & delve into > the more interesting ones. We did try that, however with the large number of sequences she needed to look up, she was black-listed from their machine. We need to find the full GenBank entry given a particular identifier, unfortunately the easiest way I've found so far seems to be the Entrez system, and that appears to not be possible to download. Is there another way to get the full genbank entry given the identifier? --- Jordan Swanson __________________________________ Do you Yahoo!? New Yahoo! Photos - easier uploading and sharing. http://photos.yahoo.com/ --__--__-- Message: 2 Date: Thu, 18 Dec 2003 13:00:25 -0800 From: Iddo Friedberg To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Is it possible to Blast against genBank files Reply-To: bio_bulletin_board at bioinformatics.org Biopython has something that can do that. Maybe Bioperl too. Let me know if you want the Python code. ./I jordan swanson wrote: >>You mean that the BLAST results only have the Fasta >>file annotation in >>them. Well, AFAIK, the only input to formatdb is >>Fasta or ASN.1. The >>output, anyhow, would be a one-liner. >> >>How about giving her the output in HTML (-T option)? >>blast automatically >>builds a link from each hit to the NCBI page. So >>using a browser, your >>coworker can skim the one-line annotation, and then >>click & delve into >>the more interesting ones. > > > We did try that, however with the large number of > sequences she needed to look up, she was black-listed > from their machine. We need to find the full GenBank > entry given a particular identifier, unfortunately the > easiest way I've found so far seems to be the Entrez > system, and that appears to not be possible to > download. Is there another way to get the full > genbank entry given the identifier? > > --- > Jordan Swanson > > __________________________________ > Do you Yahoo!? > New Yahoo! Photos - easier uploading and sharing. > http://photos.yahoo.com/ > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://ffas.ljcrf.edu/~iddo --__--__-- Message: 3 Date: Thu, 18 Dec 2003 17:01:20 -0500 From: Boris Steipe To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] Is it possible to Blast against genBank files Reply-To: bio_bulletin_board at bioinformatics.org jordan swanson wrote: > > > You mean that the BLAST results only have the Fasta > > file annotation in > > them. Well, AFAIK, the only input to formatdb is > > Fasta or ASN.1. The > > output, anyhow, would be a one-liner. > > > > How about giving her the output in HTML (-T option)? > > blast automatically > > builds a link from each hit to the NCBI page. So > > using a browser, your > > coworker can skim the one-line annotation, and then > > click & delve into > > the more interesting ones. > > We did try that, however with the large number of > sequences she needed to look up, she was black-listed > from their machine. We need to find the full GenBank > entry given a particular identifier, unfortunately the > easiest way I've found so far seems to be the Entrez > system, and that appears to not be possible to > download. Is there another way to get the full > genbank entry given the identifier? > > --- > Jordan Swanson Yes, you can get the files through the SeqHound remote Perl API - easy to program and no blacklists. See: and especially: Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe --__--__-- _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board End of BiO_Bulletin_Board Digest ===== Venkata Pardhasaradhi Satagopam, Bioinformatics Scientist, Genomics IT Research, Office Address :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414 Home Address :Fritz-Frey-Str.8/112.301.01, 69121 HEIDELBERG, GERMANY. Tel:0049-(0)6221 729667 (Mobile):0049-(0)179 7927494 From boris.steipe at utoronto.ca Fri Dec 19 16:07:30 2003 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Fri, 19 Dec 2003 16:07:30 -0500 Subject: [BiO BB] RE: References: <200312191756.hBJHuMa10990@admin05.lion-ag.de> Message-ID: <3FE36891.D67B7FA1@utoronto.ca> Venkata Satagopam wrote: > > Yes, you can get the full entry of GenBank > from any public SRS servers. Here is the > link where you can found many public SRS > servers.. > http://www.lionbio.co.uk/publicsrs.html > > OR you can look at http://igbmc.u-strasbg.fr/srs6/ > > regards > venkata Yes, that too ... but SeqHound is open source, unlimited use, whereas your company markets SRS for profit under restricted terms od use. SeqHound: Licesne: GPL SRS terms of use : Respectfully, Boris ======================================== > > -----Original Message----- > From: > Posted At: Tuesday, January 01, 1991 1:00 AM > Posted To: Inbox > Conversation: > Subject: > > When replying, PLEASE edit your Subject line so it is more specific > than "Re: BiO_Bulletin_Board digest, Vol..." And, PLEASE delete any > unrelated text from the body. > > Today's Topics: > > 1. Re: Is it possible to Blast against genBank files (jordan swanson) > 2. Re: Is it possible to Blast against genBank files (Iddo Friedberg) > 3. Re: Is it possible to Blast against genBank files (Boris Steipe) > > --__--__-- > > Message: 1 > Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST) > From: jordan swanson > Subject: Re: [BiO BB] Is it possible to Blast against genBank files > To: bio_bulletin_board at bioinformatics.org > Reply-To: bio_bulletin_board at bioinformatics.org > > > You mean that the BLAST results only have the Fasta > > file annotation in > > them. Well, AFAIK, the only input to formatdb is > > Fasta or ASN.1. The > > output, anyhow, would be a one-liner. > > > > How about giving her the output in HTML (-T option)? > > blast automatically > > builds a link from each hit to the NCBI page. So > > using a browser, your > > coworker can skim the one-line annotation, and then > > click & delve into > > the more interesting ones. > > We did try that, however with the large number of > sequences she needed to look up, she was black-listed > from their machine. We need to find the full GenBank > entry given a particular identifier, unfortunately the > easiest way I've found so far seems to be the Entrez > system, and that appears to not be possible to > download. Is there another way to get the full > genbank entry given the identifier? > > --- > Jordan Swanson > > __________________________________ > Do you Yahoo!? > New Yahoo! Photos - easier uploading and sharing. > http://photos.yahoo.com/ > > --__--__-- > > Message: 2 > Date: Thu, 18 Dec 2003 13:00:25 -0800 > From: Iddo Friedberg > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Is it possible to Blast against genBank files > Reply-To: bio_bulletin_board at bioinformatics.org > > Biopython has something that can do that. Maybe Bioperl too. Let me know > if you want the Python code. > > ./I > > jordan swanson wrote: > >>You mean that the BLAST results only have the Fasta > >>file annotation in > >>them. Well, AFAIK, the only input to formatdb is > >>Fasta or ASN.1. The > >>output, anyhow, would be a one-liner. > >> > >>How about giving her the output in HTML (-T option)? > >>blast automatically > >>builds a link from each hit to the NCBI page. So > >>using a browser, your > >>coworker can skim the one-line annotation, and then > >>click & delve into > >>the more interesting ones. > > > > > > We did try that, however with the large number of > > sequences she needed to look up, she was black-listed > > from their machine. We need to find the full GenBank > > entry given a particular identifier, unfortunately the > > easiest way I've found so far seems to be the Entrez > > system, and that appears to not be possible to > > download. Is there another way to get the full > > genbank entry given the identifier? > > > > --- > > Jordan Swanson > > > > __________________________________ > > Do you Yahoo!? > > New Yahoo! Photos - easier uploading and sharing. > > http://photos.yahoo.com/ > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > > -- > Iddo Friedberg, Ph.D. > The Burnham Institute > 10901 N. Torrey Pines Rd. > La Jolla, CA 92037 > USA > Tel: +1 (858) 646 3100 x3516 > Fax: +1 (858) 646 3171 > http://ffas.ljcrf.edu/~iddo > > --__--__-- > > Message: 3 > Date: Thu, 18 Dec 2003 17:01:20 -0500 > From: Boris Steipe > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] Is it possible to Blast against genBank files > Reply-To: bio_bulletin_board at bioinformatics.org > > jordan swanson wrote: > > > > > You mean that the BLAST results only have the Fasta > > > file annotation in > > > them. Well, AFAIK, the only input to formatdb is > > > Fasta or ASN.1. The > > > output, anyhow, would be a one-liner. > > > > > > How about giving her the output in HTML (-T option)? > > > blast automatically > > > builds a link from each hit to the NCBI page. So > > > using a browser, your > > > coworker can skim the one-line annotation, and then > > > click & delve into > > > the more interesting ones. > > > > We did try that, however with the large number of > > sequences she needed to look up, she was black-listed > > from their machine. We need to find the full GenBank > > entry given a particular identifier, unfortunately the > > easiest way I've found so far seems to be the Entrez > > system, and that appears to not be possible to > > download. Is there another way to get the full > > genbank entry given the identifier? > > > > --- > > Jordan Swanson > > Yes, you can get the files through the SeqHound remote Perl API - easy to > program and no blacklists. > > See: > and especially: > > Best regards, > > Boris > > --- > Boris Steipe > University of Toronto > Program in Proteomics & Bioinformatics > Departments of Biochemistry & Molecular and Medical Genetics > http://biochemistry.utoronto.ca/steipe > > --__--__-- > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > End of BiO_Bulletin_Board Digest > ===== > Venkata Pardhasaradhi Satagopam, > Bioinformatics Scientist, > Genomics IT Research, > Office Address :LION Bioscience AG, Waldhofer Str.98,69123 Heidelberg,GERMANY. Tel: 0049-(0)6221 4038 414 > Home Address :Fritz-Frey-Str.8/112.301.01, > 69121 HEIDELBERG, GERMANY. Tel:0049-(0)6221 729667 > (Mobile):0049-(0)179 7927494 > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From gene.quantification at wzw.tum.de Fri Dec 19 06:43:01 2003 From: gene.quantification at wzw.tum.de (qPCR 2004 Symposium - Gene Quantification Newsletter) Date: Fri, 19 Dec 2003 12:43:01 +0100 Subject: [BiO BB] Preliminary qPCR 2004 Symposium Agenda Message-ID: <5.2.1.1.0.20031219124244.028abd78@pollux.wzw.tum.de> First International qPCR Symposium & Application Workshop Transcriptomics, Clinical Diagnostics & Gene Quantification 3rd - 6th March, 2004 in Freising-Weihenstephan, Germany http://www.wzw.tum.de/gene-quantification/qpcr2004/index.shtml Now available - Preliminary Symposium Agenda 70 internationally renown speakers will be participating in a lively and exciting programme enabling the valuable exchange of information in the qPCR field. http://www.wzw.tum.de/gene-quantification/qpcr2004/preliminary-symposium-agenda.pdf Up to now around 150 Abstracts submitted from 31 Nations worldwide http://www.wzw.tum.de/gene-quantification/qpcr2004/main-2004.shtml#news The Symposium and the Application Workshop presents unbiased international lectures & posters about quantification strategies, normalisation methods & new algorithms for exact nucleic acid quantification in the broad range of qPCR applications: Transcriptomics, Clinical Diagnostics, Food Hygiene & GMO, Expression profiling, Microbiology, Pharmacogenomics, Forensic, Nutrigenomics, Molecular Endocrinology, cDNA Array Verification, Theoretical qPCR, Pre-analytical Steps & RT, Isolation of Nucleic Acids. http://www.wzw.tum.de/gene-quantification/qpcr2004/qpcr2004-workshop.html Parallel to the Symposium an Industrial Exhibition will take place along with the congress, where an intensive conversation with numerous companies is possible (real-time PCR Cyclers, Kit Producers, Nucleic Acid Purification Systems, Enzyme Producers, Plastic ware Suppliers, etc.). 25 companies agreed to participate at the Industrial Exhibition. http://www.wzw.tum.de/gene-quantification/qpcr2004/companies.html The organization team thank all Sponsors of the Symposium: http://www.wzw.tum.de/gene-quantification/qpcr2004/qpcr2004-sponsors.html Platinum Sponsor Roche Diagnostics Gold Sponsor BioRad Gold Sponsor MJ Research Silver Sponsor ABI Applied Biosystems Silver Sponsor Eurogentec Silver Sponsor Invitrogen Silver Sponsor Premier Biosoft Silver Sponsor Qiagen Silver Sponsor Roboscreen & Invitek Silver Sponsor Stratagene Symposium registration: Registration Form (PDF) http://www.wzw.tum.de/gene-quantification/qpcr2004/registration.pdf Registration Form (DOC) http://www.wzw.tum.de/gene-quantification/qpcr2004/registration.doc Peaceful Christmas and a happy NEW YEAR 2004 Michael Pfaffl ******************************************************************************************** Gene.Quantification @ wzw.tum.de e-mail: gene.quantification at wzw.tum.de homepage: http://www.wzw.tum.de/gene-quantification/index.shtml homepage: http://www.wzw.tum.de/gene-quantification/physiology.shtml homepage: http://www.wzw.tum.de/gene-quantification/bioinformatics.shtml responsible Senior Scientist: PD Dr. Michael W. Pfaffl Physiology - Weihenstephan Life Science Center Weihenstephan, Technical University of Munich Weihenstephaner Berg 3 D-85350 Freising-Weihenstephan GERMANY ******************************************************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.groenen at home.nl Sat Dec 20 07:38:55 2003 From: peter.groenen at home.nl (Peter Groenen) Date: Sat, 20 Dec 2003 13:38:55 +0100 Subject: [BiO BB] Re: Is it possible to Blast against genBank files References: <20031219170113.50D0DD2A54@www.bioinformatics.org> Message-ID: <001a01c3c6f6$3b891580$0201a8c0@cp414223a> It seems that SRS (sequence retrieval system) is still not very well known on the other side of the Atlantic. ;-) It is for free (up to version 7 I believe, for Academic users) and is still one of the best solutions for these things (instead of starting to hack around with Perl again). SRS does it all and you can even install Blast, ClustalW within SRS if you're a little more experienced. Have a look at srs.ebi.ac.uk You'll find some more related stuff ad you can download all info and binaries from their FTP site. Be aware thta you'll need a little experience to administrate the application. But you'll succeed pretty quick. ----- Original Message ----- From: bio_bulletin_board-request at bioinformatics.org To: bio_bulletin_board at bioinformatics.org Sent: Friday, December 19, 2003 6:01 PM Subject: BiO_Bulletin_Board digest, Vol 1 #590 - 3 msgs Date: Thu, 18 Dec 2003 12:53:51 -0800 (PST) From: jordan swanson Subject: Re: [BiO BB] Is it possible to Blast against genBank files To: bio_bulletin_board at bioinformatics.org Reply-To: bio_bulletin_board at bioinformatics.org > You mean that the BLAST results only have the Fasta > file annotation in > them. Well, AFAIK, the only input to formatdb is > Fasta or ASN.1. The > output, anyhow, would be a one-liner. > > How about giving her the output in HTML (-T option)? > blast automatically > builds a link from each hit to the NCBI page. So > using a browser, your > coworker can skim the one-line annotation, and then > click & delve into > the more interesting ones. We did try that, however with the large number of sequences she needed to look up, she was black-listed from their machine. We need to find the full GenBank entry given a particular identifier, unfortunately the easiest way I've found so far seems to be the Entrez system, and that appears to not be possible to download. Is there another way to get the full genbank entry given the identifier? --- Jordan Swanson __________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: From peter.groenen at home.nl Sat Dec 20 10:47:15 2003 From: peter.groenen at home.nl (Peter Groenen) Date: Sat, 20 Dec 2003 16:47:15 +0100 Subject: [BiO BB] Re: SRS References: <20031220124126.EA251D29D2@www.bioinformatics.org> Message-ID: <001501c3c710$8a960ec0$0201a8c0@cp414223a> There's no comparison between something like Seqhound and SRS. Moreover, it's free. Unless you prefer hacking instead of science...;-) Peter Venkata Satagopam wrote: > > Yes, you can get the full entry of GenBank > from any public SRS servers. Here is the > link where you can found many public SRS > servers.. > http://www.lionbio.co.uk/publicsrs.html > > OR you can look at http://igbmc.u-strasbg.fr/srs6/ > > regards > venkata Yes, that too ... but SeqHound is open source, unlimited use, whereas your company markets SRS for profit under restricted terms od use. SeqHound: Licesne: GPL SRS terms of use : Respectfully, Boris ======================================== -------------- next part -------------- An HTML attachment was scrubbed... URL: From mgollery at unr.edu Sun Dec 21 00:08:30 2003 From: mgollery at unr.edu (Martin Gollery) Date: Sat, 20 Dec 2003 21:08:30 -0800 Subject: [BiO BB] Re: SRS In-Reply-To: <001501c3c710$8a960ec0$0201a8c0@cp414223a> References: <20031220124126.EA251D29D2@www.bioinformatics.org> <001501c3c710$8a960ec0$0201a8c0@cp414223a> Message-ID: <1071983310.3fe52acef2451@webmail.unr.edu> The latest version even has links to GeneSpring- very cool, very powerful. I am looking forward to playing with it when I get a chance! Marty Quoting Peter Groenen : > There's no comparison between something like Seqhound and SRS. Moreover, it's > free. Unless you prefer hacking instead of science...;-) > Peter > > Venkata Satagopam wrote: > > > > Yes, you can get the full entry of GenBank > > from any public SRS servers. Here is the > > link where you can found many public SRS > > servers.. > > http://www.lionbio.co.uk/publicsrs.html > > > > OR you can look at http://igbmc.u-strasbg.fr/srs6/ > > > > regards > > venkata > > Yes, that too ... but SeqHound is open source, unlimited use, whereas your > company markets SRS for profit under restricted terms od use. > > > SeqHound: Licesne: GPL > SRS terms of use : > > > Respectfully, > > Boris > ======================================== > > Martin Gollery Associate Director Center For Bioinformatics University of Nevada at Reno Dept. of Biochemistry / MS330 775-784-7042 ------------------------------------------------- This mail sent through https://webmail.unr.edu From sharmash at pn2.vsnl.net.in Wed Dec 24 22:59:40 2003 From: sharmash at pn2.vsnl.net.in (SH Sharma) Date: Thu, 25 Dec 2003 09:29:40 +0530 Subject: [BiO BB] guidance needed Message-ID: <001201c3ca9b$85e62520$b45941db@sharmash> hi we are computer engineering students developing a a sequence retreival system to retreive data from genbank. This is how we have thought of (1) first we will have our software running on apache web server. The webserver will accept http requests from the web browsers from different clients. To handle this we will be running PHP script on the web server. (2) on getting a request now we want our software to access data from GenBANK. How to achieve this. what technolgy is needed to get data from a remote bioinformatics database such as Genbank or swiss prot and save the data in the local database. We would be thankful if you can guide us. Neeraj sharma B.E. computer engineering university of pune india -------------- next part -------------- An HTML attachment was scrubbed... URL: From bgrs2004 at bionet.nsc.ru Thu Dec 25 05:13:47 2003 From: bgrs2004 at bionet.nsc.ru (BGRS2004 Committee) Date: Thu, 25 Dec 2003 16:13:47 +0600 Subject: [BiO BB] BGRS'2004 Message-ID: Dear Colleague: Program and Organizing Committees have honor to announce the traditional biennial event-The Fourth International Conference on Bioinformatics of Genome Regulation and Structure (BGRS'2004)-to be held on July 25-30, 2004, in Akademgorodok, Novosibirsk, Russia. Do put it in your diary, please! BGRS'2004 is a multidisciplinary conference, and we are pleased to invite scientists with an interest in bioinformatics, mathematical, theoretical, or computational biology to attend the meeting. Its scope includes development and application of advanced methods of computational and theoretical analysis to structure-function genome organization, proteomics, and evolutionary and system biology. The event addresses the latest research in these fields, and will be a great opportunity for attendees to showcase their works. BGRS'2004 provides a general forum for disseminating and facilitating the latest developments in bioinformatics in molecular biology, and we also invite scientists participating in experimental research and using theoretical and/or computational methods in their practice and/or researchers supported by INTAS grants to come. We will be delighted to see industry representatives from biotechnology and pharmaceutical companies as BGRS'2004 conferees, too. Find, please, more detailed information in the attached file or at the official site of the conference http://www.bionet.nsc.ru/meeting/bgrs2004/anouncement.html We would be very grateful if you could spread this information among your colleagues who also could be interested in attending the Conference. We do hope that you will be able to participate in the Conference, and try our best for your visit to be pleasant and fruitful. Merry Christmas and happy New Year! Looking forward to see you in Novosibirsk, Program/Organizing Committees -------------- next part -------------- A non-text attachment was scrubbed... Name: Inf_Letter 1_rev.doc Type: application/msword Size: 24064 bytes Desc: not available URL: From B.A.T.Svensson at lumc.nl Sun Dec 28 06:14:49 2003 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Sun, 28 Dec 2003 12:14:49 +0100 Subject: [BiO BB] guidance needed Message-ID: Question on (2): Do you want to store and process data localy? -----Original Message----- From: SH Sharma To: bio_bulletin_board at bioinformatics.org Sent: 2003-12-25 04:59 Subject: [BiO BB] guidance needed hi we are computer engineering students developing a a sequence retreival system to retreive data from genbank. This is how we have thought of (1) first we will have our software running on apache web server. The webserver will accept http requests from the web browsers from different clients. To handle this we will be running PHP script on the web server. (2) on getting a request now we want our software to access data from GenBANK. How to achieve this. what technolgy is needed to get data from a remote bioinformatics database such as Genbank or swiss prot and save the data in the local database. We would be thankful if you can guide us. Neeraj sharma B.E. computer engineering university of pune india From venkata_satagopam at yahoo.com Mon Dec 29 17:49:21 2003 From: venkata_satagopam at yahoo.com (Venkata Satagopam) Date: Mon, 29 Dec 2003 14:49:21 -0800 (PST) Subject: [BiO BB] guidance needed In-Reply-To: Message-ID: <20031229224921.47189.qmail@web20413.mail.yahoo.com> Its is better to store the data locally, and parse the data by using a parser and store the indices in token tables (indexing). Use these indices to retrieve the data. "Svensson, B.A.T. (HKG)" wrote: Question on (2): Do you want to store and process data localy? -----Original Message----- From: SH Sharma To: bio_bulletin_board at bioinformatics.org Sent: 2003-12-25 04:59 Subject: [BiO BB] guidance needed hi we are computer engineering students developing a a sequence retreival system to retreive data from genbank. This is how we have thought of (1) first we will have our software running on apache web server. The webserver will accept http requests from the web browsers from different clients. To handle this we will be running PHP script on the web server. (2) on getting a request now we want our software to access data from GenBANK. How to achieve this. what technolgy is needed to get data from a remote bioinformatics database such as Genbank or swiss prot and save the data in the local database. We would be thankful if you can guide us. Neeraj sharma B.E. computer engineering university of pune india _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Venkata Pardhasaradhi Satagopam, Bioinformatician, Fritz-Frey-Str 8, 69121 Heidelberg, Germany. Tel. (Land) : +49 (0)6221 729 667 (Mobile): +49 (0)179 792 7494 --------------------------------- Do you Yahoo!? Yahoo! Photos - Get your photo on the big screen in Times Square -------------- next part -------------- An HTML attachment was scrubbed... URL: From biotechinfotech at yahoo.com Tue Dec 30 05:37:58 2003 From: biotechinfotech at yahoo.com (vinod jangir) Date: Tue, 30 Dec 2003 02:37:58 -0800 (PST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #595 - 1 msg In-Reply-To: <20031228170106.57F0BD2A2B@www.bioinformatics.org> Message-ID: <20031230103758.59783.qmail@web20419.mail.yahoo.com> hi.. i am working seriously in the field of bioinformatics.. i can help u.. in any type of matter relating the networks and hardware mail me what type of help u need.... i am doing masters in the bioinformatics.. from iase university. vinod vinod kumar --------------------------------- Do you Yahoo!? Find out what made the Top Yahoo! Searches of 2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: From biotechinfotech at yahoo.com Tue Dec 30 05:37:59 2003 From: biotechinfotech at yahoo.com (vinod jangir) Date: Tue, 30 Dec 2003 02:37:59 -0800 (PST) Subject: [BiO BB] Re: BiO_Bulletin_Board digest, Vol 1 #595 - 1 msg In-Reply-To: <20031228170106.57F0BD2A2B@www.bioinformatics.org> Message-ID: <20031230103759.59791.qmail@web20419.mail.yahoo.com> hi.. i am working seriously in the field of bioinformatics.. i can help u.. in any type of matter relating the networks and hardware mail me what type of help u need.... i am doing masters in the bioinformatics.. from iase university. vinod vinod kumar --------------------------------- Do you Yahoo!? Find out what made the Top Yahoo! Searches of 2003 -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.A.T.Svensson at lumc.nl Tue Dec 30 06:44:38 2003 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Tue, 30 Dec 2003 12:44:38 +0100 Subject: [BiO BB] guidance needed Message-ID: Since the guys who asked the question are computer engineering students, they would (read: should) rather use a RDBMS to store data locally. -----Original Message----- From: Venkata Satagopam To: bio_bulletin_board at bioinformatics.org; 'SH Sharma ' Sent: 2003-12-29 23:49 Subject: RE: [BiO BB] guidance needed Its is better to store the data locally, and parse the data by using a parser and store the indices in token tables (indexing). Use these indices to retrieve the data. "Svensson, B.A.T. (HKG)" wrote: Question on (2): Do you want to store and process data localy? -----Original Message----- From: SH Sharma To: bio_bulletin_board at bioinformatics.org Sent: 2003-12-25 04:59 Subject: [BiO BB] guidance needed hi we are computer engineering students developing a a sequence retreival system to retreive data from genbank. This is how we have thought of (1) first we will have our software running on apache web server. The webserver will accept http requests from the web browsers from different clients. To handle this we will be running PHP script on the web server. (2) on getting a request now we want our software to access data from GenBANK. How to achieve this. what technolgy is needed to get data from a remote bioinformatics database such as Genbank or swiss prot and save the data in the local database. We would be thankful if you can guide us. Neeraj sharma B.E. computer engineering university of pune india _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Venkata Pardhasaradhi Satagopam, Bioinformatician, Fritz-Frey-Str 8, 69121 Heidelberg, Germany. Tel. (Land) : +49 (0)6221 729 667 (Mobile): +49 (0)179 792 7494 _____ Do you Yahoo!? Yahoo! Photos - Get your photo on the big screen in Times Square From adrian at bioinfo.pl Tue Dec 30 05:59:55 2003 From: adrian at bioinfo.pl (Adrian Tkacz) Date: Tue, 30 Dec 2003 11:59:55 +0100 Subject: [BiO BB] guidance needed In-Reply-To: <001201c3ca9b$85e62520$b45941db@sharmash> References: <001201c3ca9b$85e62520$b45941db@sharmash> Message-ID: <1072781994.11635.24.camel@tkacz.eu.org> Hello, This link could help you: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/README?rev=1.17&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup load_seqdatabase.pl - a very flexible script to load sequences into the database Adrian Tkacz adrian at bioinfo.pl On Thu, 2003-12-25 at 04:59, SH Sharma wrote: > hi we are computer engineering students developing a a sequence > retreival system to retreive data from genbank. > This is how we have thought of > (1) first we will have our software running on apache web server. The > webserver will accept http requests from the web browsers from > different clients. To handle this we will be running PHP script on the > web server. > (2) on getting a request now we want our software to access data from > GenBANK. How to achieve this. what technolgy is needed to get data > from a remote bioinformatics database such as Genbank or swiss prot > and save the data in the local database. > > We would be thankful if you can guide us. > > Neeraj sharma > B.E. computer engineering > university of pune > india From sharmash at pn2.vsnl.net.in Tue Dec 30 23:04:23 2003 From: sharmash at pn2.vsnl.net.in (SH Sharma) Date: Wed, 31 Dec 2003 09:34:23 +0530 Subject: [BiO BB] how to access database remotely Message-ID: <000801c3cf53$2db3d020$065941db@sharmash> We are a group (5) computer engineering students.We are developing our own Sequence retrieval system. We have the following queries. (1) We want to access and then search the Genbank or EMBL or Swissprot database. (2) Hence do we need any permission. (3)If not what is the location or path where the respective repository for Genbank, EMBL or swissprot is located. -------------- next part -------------- An HTML attachment was scrubbed... URL: From B.A.T.Svensson at lumc.nl Wed Dec 31 05:42:36 2003 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Wed, 31 Dec 2003 11:42:36 +0100 Subject: [BiO BB] guidance needed Message-ID: Swissprot: http://www.expasy.org/expasy_urls.html GeneBank: http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html EMBL: http://www.ebi.ac.uk/embl/Access/index.html -----Original Message----- From: SH Sharma To: Svensson, B.A.T. (HKG) Sent: 2003-12-30 19:02 Subject: Re: [BiO BB] guidance needed Respected Sir, We are thankful to the valuable advice we are receiving. IS IT POSSIBLE TO REMOTELY SEARCH AND RETRIEVE DATA FROM THE EMBL OR GENBANK OR SWISSPROT DATATBASE USING OUR OWN RETRIEVAL SYSTEM. (we wish to develo our own retrieval system even though Entrez and several others are available) If yes then do we have to take permission or need to pay. If no then is it that we have to necessarily downloading the respective database. ----- Original Message ----- From: "Svensson, B.A.T. (HKG)" To: Cc: "''SH Sharma ' '" Sent: Tuesday, December 30, 2003 5:14 PM Subject: RE: [BiO BB] guidance needed > Since the guys who asked the question are computer engineering students, > they would (read: should) rather use a RDBMS to store data locally. > > -----Original Message----- > From: Venkata Satagopam > To: bio_bulletin_board at bioinformatics.org; 'SH Sharma ' > Sent: 2003-12-29 23:49 > Subject: RE: [BiO BB] guidance needed > > Its is better to store the data locally, and parse the data > by using a parser and store the indices in token tables (indexing). > Use these indices to retrieve the data. > > "Svensson, B.A.T. (HKG)" wrote: > > Question on (2): > > Do you want to store and process data localy? > > -----Original Message----- > From: SH Sharma > To: bio_bulletin_board at bioinformatics.org > Sent: 2003-12-25 04:59 > Subject: [BiO BB] guidance needed > > hi we are computer engineering students developing a a sequence > retreival system to retreive data from genbank. > This is how we have thought of > (1) first we will have our software running on apache web server. The > webserver will accept http requests from the web browsers from different > clients. To handle this we will be running PHP script on the web server. > (2) on getting a request now we want our software to access data from > GenBANK. How to achieve this. what technolgy is needed to get data from > a remote bioinformatics database such as Genbank or swiss prot and save > the data in the local database. > > We would be thankful if you can guide us. > > Neeraj sharma > B.E. computer engineering > university of pune > india > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > Venkata Pardhasaradhi Satagopam, > Bioinformatician, > Fritz-Frey-Str 8, 69121 Heidelberg, Germany. > Tel. (Land) : +49 (0)6221 729 667 > (Mobile): +49 (0)179 792 7494 > > > _____ > > Do you Yahoo!? > Yahoo! Photos - Get your photo on the big screen in Times Square > implenol?.file=ny_ts_splash.html> From B.A.T.Svensson at lumc.nl Wed Dec 31 05:55:09 2003 From: B.A.T.Svensson at lumc.nl (Svensson, B.A.T. (HKG)) Date: Wed, 31 Dec 2003 11:55:09 +0100 Subject: [BiO BB] how to access database remotely Message-ID: If you point a web browser to those data centers I am quite confident that you will be able to get an answer on all your question below. Try out: * http://www.ncbi.nlm.nih.gov/Genbank/ * http://www.expasy.org/sprot/ * http://www1.embl-heidelberg.de/ Swissprot have copyright on their data, and you should read the copyright notice before using the data. Depending on how you want to use swissprot, you might need to have permission from them. -----Original Message----- From: SH Sharma To: bio_bulletin_board at bioinformatics.org Sent: 2003-12-31 05:04 Subject: [BiO BB] how to access database remotely We are a group (5) computer engineering students.We are developing our own Sequence retrieval system. We have the following queries. (1) We want to access and then search the Genbank or EMBL or Swissprot database. (2) Hence do we need any permission. (3)If not what is the location or path where the respective repository for Genbank, EMBL or swissprot is located. From idoerg at burnham.org Wed Dec 31 12:24:40 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 31 Dec 2003 09:24:40 -0800 Subject: [BiO BB] how to access database remotely In-Reply-To: <000801c3cf53$2db3d020$065941db@sharmash> References: <000801c3cf53$2db3d020$065941db@sharmash> Message-ID: <3FF30658.3060007@burnham.org> Regarding GenBank: Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html Access restrictions -- for bandwidth, not for intellectual property reasons -- are listed there. Expasy documentation is here: http://us.expasy.org/doc.html SH Sharma wrote: > We are a group (5) computer engineering students.We are developing our > own Sequence retrieval system. We have the following queries. > (1) We want to access and then search the Genbank or EMBL or Swissprot > database. > (2) Hence do we need any permission. > (3)If not what is the location or path where the respective repository > for Genbank, EMBL or swissprot is located. -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 713 9930 http://ffas.ljcrf.edu/~iddo From dmb at mrc-dunn.cam.ac.uk Wed Dec 31 12:34:38 2003 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Wed, 31 Dec 2003 17:34:38 -0000 (GMT) Subject: [BiO BB] how to access database remotely In-Reply-To: <000801c3cf53$2db3d020$065941db@sharmash> References: <000801c3cf53$2db3d020$065941db@sharmash> Message-ID: <33413.80.1.204.145.1072892078.squirrel@www.mrc-dunn.cam.ac.uk> ++ SH Sharma-- > We are a group (5) computer engineering students.We are developing our own > Sequence retrieval system. We have the following queries. (1) We want to access > and then search the Genbank or EMBL or Swissprot database. (2) Hence do we need > any permission. > (3)If not what is the location or path where the respective repository for > Genbank, EMBL or swissprot is located. Hi, I regularly download SP/TrEMBL sequence databases and parse them into RDB using the SwissKnife tool. I think this is OK regarding the copyright as I use the database for research and not industrial app. Please let me know if you find any problems here. I would be happy to help develop a PHP interface to the underlying RDB - I like the 'shopping basket' approach to bio data analysis. Cheers, Dan. From micheld at mshri.on.ca Sat Dec 6 13:38:31 2003 From: micheld at mshri.on.ca (Michel Dumontier) Date: Sat, 6 Dec 2003 13:38:31 -0500 Subject: [BiO BB] Structure/Sequence Alignment References: Message-ID: <034c01c3bc28$32cbb2f0$3afac5c0@moose> Pankaj, Try using ClustalW. It lets you load in the structure template's secondary structure as a numeric profile that weighs position-specific gap penalties. This typically forces gaps into unstructured regions of the protein structure. You can make a multiple sequence alignment of the sequences and then generate a profile-profile alignment. -=Michel=- ----- Original Message ----- From: "Pankaj" To: Sent: Tuesday, January 06, 2004 10:35 AM Subject: [BiO BB] hi > hi all, > i m a new member of this board. > i have a 3 protein structures (all taking the same fold) with the > substrate bound. the residues surrounding the substrate are the active > site residues. now i have a set of 400 protein sequences which i know > take the same above mentioned fold. i want to extract the active site > residues from these 400 sequences. but whatever alignment program i > use either uses only sequence information or only structure > information. is there an alignment program which can use both > structure and sequence information for the alignment of these 400 > sequences on the strcutural template >