From jasoncting at hotmail.com Wed Sep 1 22:57:41 2004 From: jasoncting at hotmail.com (Jason Ting) Date: Wed, 1 Sep 2004 22:57:41 -0400 Subject: [BiO BB] remove References: <20040828143317.26750.qmail@webmail-2-5.mesa1.secureserver.net> Message-ID: Please remove me from your mailing list. Thank you. J.Ting ----- Original Message ----- From: information at virtualgenomics.org To: bio_bulletin_board at bioinformatics.org Sent: Saturday, August 28, 2004 10:33 AM Subject: [BiO BB] Fourth Virtual Genomics and Bioinformatics Conference Fourth Virtual Conference on Genomics and Bioinformatics September 21-24, 2004 www.virtualgenomics.org/conference_2004.htm *********************************************************************** Location: Virtual Locations Worldwide (List available at www.virtualgenomics.org/conference_2004.htm) Registration fees: None The Virtual Conference on Genomics and Bioinformatics is an advanced collaborative environment featuring high profile researchers involved in the development and use of cutting edge technologies and approaches which allow a better understanding of the molecular structure and dynamics of biological systems. The objectives of the conference are: * Transcend geographical and economical barriers for the exchange of ideas that facilitates the interaction and collaboration among scientists and educators around the world. * Address the benefits and limitations of the newest developments in post-genomic technologies. * Explore the social and ethical implications of genomic and bioinformatic research. * Establish new ways to introduce the high school community to today's multidisciplinary science. Speakers: Uri Alon, Weizmann Institute of Science. Israel Wanda Andreoni, IBM Z?rich Research Laboratory, Switzerland Kim Baldridge, Universit?t Z?rich. Switzerland Patsy Babbitt. University of California, San Francisco. USA Irene Bosch, University of Massachusetts Medical School. USA Carlos Camacho, University of Pittsburgh, USA Colin C. Collins, Medicine and Cancer Research Institute, UCSF. USA Charles DeLisi, Boston University. USA Martin Gollery, University of Nevada at Reno. USA Fern Hunt, National Institute of Standards and Technology. USA S.S. Iyengar, Louisiana State University. USA Maricel Kann, National Institutes of Health. NCBI. USA Eugene Koonin, National Institutes of Health. USA Luis Rocha, Los Alamos National Laboratory. USA John B. Shabb, University of North Dakota. USA Wibke Sudholt, Universit?t Z?rich. Switzerland Christoph W. Sensen, University of Calgary. Canada Richard Simon, National Institutes of Health. NCI. USA Jason Suen, California Institute of Technology, USA Sarah B. Tegen, National Academy of Sciences, USA William Perrizo, North Dakota State University. USA Willy Valdivia-Granda. Orion Integrated Biosciences. USA Yuzhen Ye, The Burnham Institute. USA Roie Yerushalmi, Weizmann Institute of Science. Israel For more information visit www.virtualgenomics.org/conference_2004.htm _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -------------- next part -------------- An HTML attachment was scrubbed... URL: From rls at cin.ufpe.br Fri Sep 3 08:39:36 2004 From: rls at cin.ufpe.br (rls at cin.ufpe.br) Date: Fri, 3 Sep 2004 09:39:36 -0300 (BRT) Subject: [BiO BB] remove In-Reply-To: References: <20040828143317.26750.qmail@webmail-2-5.mesa1.secureserver.net> Message-ID: <2004.172.17.70.13.1094215176.squirrel@webmail.cin.ufpe.br> Please remove me too Rafael Luiz > Please remove me from your mailing list. > > Thank you. > > J.Ting > ----- Original Message ----- > From: information at virtualgenomics.org > To: bio_bulletin_board at bioinformatics.org > Sent: Saturday, August 28, 2004 10:33 AM > Subject: [BiO BB] Fourth Virtual Genomics and Bioinformatics Conference > > > Fourth Virtual Conference on Genomics and Bioinformatics > September 21-24, 2004 > www.virtualgenomics.org/conference_2004.htm > *********************************************************************** > Location: Virtual Locations Worldwide (List available at > www.virtualgenomics.org/conference_2004.htm) > Registration fees: None > > The Virtual Conference on Genomics and Bioinformatics is an advanced > collaborative environment featuring high profile researchers involved > in the development and use of cutting edge technologies and approaches > which allow a better understanding of the molecular structure and > dynamics of biological systems. The objectives of the conference are: > > * Transcend geographical and economical barriers for the exchange of > ideas that facilitates the interaction and collaboration among > scientists and educators around the world. > * Address the benefits and limitations of the newest developments in > post-genomic technologies. > * Explore the social and ethical implications of genomic and > bioinformatic research. > * Establish new ways to introduce the high school community to today's > multidisciplinary science. > > Speakers: > > Uri Alon, Weizmann Institute of Science. Israel > Wanda Andreoni, IBM Z?rich Research Laboratory, Switzerland > Kim Baldridge, Universit?t Z?rich. Switzerland > Patsy Babbitt. University of California, San Francisco. USA > Irene Bosch, University of Massachusetts Medical School. USA > Carlos Camacho, University of Pittsburgh, USA > Colin C. Collins, Medicine and Cancer Research Institute, UCSF. USA > Charles DeLisi, Boston University. USA > Martin Gollery, University of Nevada at Reno. USA > Fern Hunt, National Institute of Standards and Technology. USA > S.S. Iyengar, Louisiana State University. USA > Maricel Kann, National Institutes of Health. NCBI. USA > Eugene Koonin, National Institutes of Health. USA > Luis Rocha, Los Alamos National Laboratory. USA > John B. Shabb, University of North Dakota. USA > Wibke Sudholt, Universit?t Z?rich. Switzerland > Christoph W. Sensen, University of Calgary. Canada > Richard Simon, National Institutes of Health. NCI. USA > Jason Suen, California Institute of Technology, USA > Sarah B. Tegen, National Academy of Sciences, USA > William Perrizo, North Dakota State University. USA > Willy Valdivia-Granda. Orion Integrated Biosciences. USA > Yuzhen Ye, The Burnham Institute. USA > Roie Yerushalmi, Weizmann Institute of Science. Israel > > For more information visit www.virtualgenomics.org/conference_2004.htm > _______________________________________________ BiO_Bulletin_Board > maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From ian.donaldson at mshri.on.ca Thu Sep 2 15:18:26 2004 From: ian.donaldson at mshri.on.ca (Ian Donaldson) Date: Thu, 2 Sep 2004 15:18:26 -0400 Subject: [BiO BB] SeqHound release v3.0 now available Message-ID: <490D0AFAF3D2D3119F6C00508B6FDF150690F78E@ex.mshri.on.ca> Dear all: SeqHound v3.0 is available for download now from http://www.blueprint.org/seqhound/api_help/seqhound_help_guides.html. Major changes to this release include a port to a MySQL database backend allowing users to install a virtually free bioinformatics-programming platform in-house using instructions provided in the SeqHound Manual. The remote API (available in Java and Perl) is now supported by a FastCGI server for even faster response times. We are interested in identifying developers who are already using SeqHound. If you are, please sign up for the seqhound.usergroup email list at http://lists.blueprint.org/mailman/listinfo/seqhound.usergroup. Feedback and discussions on future development are welcome at this list. Best regards, Ian Ian Donaldson, Ph.D. Manager of Bioinformatics Software Development The Blueprint Initiative - North America 522 University Ave. Toronto, Ontario, Canada M5G 1W7 http://blueprint.org ian.donaldson at blueprint.org About SeqHound SeqHound is a freely available bioinformatics database warehouse resource. Over 300 Gigabytes of data are collected, integrated and updated from around the world on a nightly basis. Sources include the National Center for Biotechnology Information and the Gene Ontology Consortium. Programmers have unrestricted access to up-to-date data via a remote Application Programming Interface (API) written in Perl, Java, C and C++. Over 150 function calls allow access to the complete collection of GenBank, RefSeq and SwissProt sequences, 3-D structures, precomputed protein neighbours, redundancies and conserved domain analyses. Users may also access collected sequence annotations including taxonomy, Gene Ontology assignments and PubMed links. All functions are fully documented and tested on a daily basis. The Blueprint SeqHound server is supported by a redundant architecture (failover load-balancers, failover servers and, failover SANs) for complete fault protection against component failure and to ensure rapid response time. SeqHound encourages unrestricted 24x7 calls to its servers, to allow programmers rapid, uninterrupted, access to biological data on a global basis. SeqHound services over 700,000 hits per day. All SeqHound code is freely distributed under the GNU Public License. Find SeqHound at www.blueprint.org. From dmb at mrc-dunn.cam.ac.uk Tue Sep 7 12:20:59 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 7 Sep 2004 17:20:59 +0100 (BST) Subject: [BiO BB] Structural genomics and PDB growth? In-Reply-To: <20040811075317.91221.qmail@web41605.mail.yahoo.com> Message-ID: On Wed, 11 Aug 2004, Iddo Friedberg wrote: > >--- Dan Bolser wrote: > >> On Mon, 9 Aug 2004, Iddo Friedberg wrote: >> >> >Hi Dan, >> > >> >For your first question: >> > >> >We published something in PSB'04 >> > >> >http://helix-web.stanford.edu/psb04/bourne.pdf >> >> Cheers. >> >> > >> >I don't know about definitive, but it is fairly exhaustive, based >> on >> >data which was up-to-date for summer 2003. >> > >> >PDB will keep growing as long as crystallographers/NMR people have >> >jobs and have families to feed. Future growth rate, as always, is >> >estimated by extrapolation. However, come the technological >> >breakthrough whcih will enable faster solutions for membrane >> >proteins, the growth rate will probably increase :) >> >> That is the thing, but is the rate of increase increasing? > > >I'm not sure by what you mean by "an increasing rate of increase". >PDB growth is exponential. What is the exponent? Any citation on this? When I say 'increasing increase' I mean (I think) an increasing exponent over time, something like a double exponential. This looks interesting... http://www.npaci.edu/online/v6.4/pdb.predict.html http://cubic.bioc.columbia.edu/papers/1998_marrying/paper.html I haven't had time to look in detail at the replies I got from this query, so thanks for those. I will try to summarize them when I do. Cheers, Dan. > >./I > >> >> >Cheers, >> > >> >Iddo >> > >> > >> > >> >--- Dan Bolser wrote: >> > >> >> >> >> Can anyone point me at definative literature for estimates of >> PDB >> >> growth >> >> and the impact of structural genomics? >> >> >> >> What evidence do we have that the PDB will keep growing? What is >> >> the best >> >> current estimate of that growth rate? >> >> >> >> Cheers, >> >> Dan. >> >> >> >> >> >> _______________________________________________ >> >> BiO_Bulletin_Board maillist - >> >> BiO_Bulletin_Board at bioinformatics.org >> >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> >> > >> > >> >===== >> >-- >> >Iddo Friedberg >> >The Burnham Institute >> >10901 N. Torrey Pines Rd. >> >La Jolla, CA, 92037 >> >USA >> >T: (858) 646 3100 x3516 >> >http://ffas.ljcrf.edu/~iddo >> > >> > >> > >> >__________________________________ >> > >===== >-- >Iddo Friedberg >The Burnham Institute >10901 N. Torrey Pines Rd. >La Jolla, CA, 92037 >USA >T: (858) 646 3100 x3516 >http://ffas.ljcrf.edu/~iddo > > > > >__________________________________ >Do you Yahoo!? >New and Improved Yahoo! Mail - 100MB free storage! >http://promotions.yahoo.com/new_mail >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From alexdow at gmail.com Tue Sep 7 18:46:55 2004 From: alexdow at gmail.com (Alex Dow) Date: Tue, 7 Sep 2004 15:46:55 -0700 Subject: [BiO BB] Optimal Sequence Alignment - Affine Gap Penalty Message-ID: <7e292adf0409071546699f4466@mail.gmail.com> Hello, I'm looking for a source related to optimal alignments with an affine gap penalty. To explain my query, I assume basic knowledge of dynamic programming and affine gap penalty. Consider aligning 2 sequences. The obvious method of using dynamic programming requires 3 matrices (or, equivalently, 3 values in each cell of a single matrix), one that results from a gap in one sequence, one from a gap in the other, and one that results from a gap in neither sequence. Durbin, et al.'s Biological Sequence Analysis (1998) refers to an algorithm that uses only 2 matrices, one that results from a gap in either sequence, and one that results from a gap in neither sequence (pages 30-31). They claim that a constraint on the cost function will guarantee optimal results from this algorithm, only he offers no proof or citation. Certainly there is a paper that demonstrates this result, only I have been unable to find it. I would appreciate any information you may have on this, whether it is a citation or even an assurance that such a paper exists. Thanks, Alex From Rajkumar.Bondugula at gmail.com Wed Sep 8 17:00:11 2004 From: Rajkumar.Bondugula at gmail.com (Raj) Date: Wed, 8 Sep 2004 16:00:11 -0500 Subject: [BiO BB] Search a Profile against a sequence database Message-ID: <33e68eb104090814002b98ca56@mail.gmail.com> Hi all, I am looking for some tool that enables me to search a (custom) sequence database using the 'profile' (BLAST generated) of the query sequence rather than a query sequence itself. If anyone is aware of any such tool, please let me know. Regards, Raj From ryangolhar at hotmail.com Wed Sep 8 17:27:43 2004 From: ryangolhar at hotmail.com (Ryan Golhar) Date: Wed, 8 Sep 2004 17:27:43 -0400 Subject: [BiO BB] Search a Profile against a sequence database In-Reply-To: <33e68eb104090814002b98ca56@mail.gmail.com> Message-ID: <000001c495ea$ad899f60$d700a8c0@GOLHARMOBILE1> You can use PSI-BLAST. Generate your sequence database using formatdb from the NCBI toolkit, and then use PSI-BLAST to search your custom database using your profile... ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Raj Sent: Wednesday, September 08, 2004 5:00 PM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] Search a Profile against a sequence database Hi all, I am looking for some tool that enables me to search a (custom) sequence database using the 'profile' (BLAST generated) of the query sequence rather than a query sequence itself. If anyone is aware of any such tool, please let me know. Regards, Raj _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From Rajkumar.Bondugula at gmail.com Thu Sep 9 10:25:41 2004 From: Rajkumar.Bondugula at gmail.com (Raj) Date: Thu, 9 Sep 2004 09:25:41 -0500 Subject: [BiO BB] Search a Profile against a sequence database In-Reply-To: <000001c495ea$ad899f60$d700a8c0@GOLHARMOBILE1> References: <33e68eb104090814002b98ca56@mail.gmail.com> <000001c495ea$ad899f60$d700a8c0@GOLHARMOBILE1> Message-ID: <33e68eb104090907256d114b23@mail.gmail.com> Golhar, I need a gapless alignment. PSIBLAST does not have a gapless alignment option. Thanks for the answer though. Regards, Raj On Wed, 8 Sep 2004 17:27:43 -0400, Ryan Golhar wrote: > You can use PSI-BLAST. Generate your sequence database using formatdb > from the NCBI toolkit, and then use PSI-BLAST to search your custom > database using your profile... > > ----- > Ryan Golhar > Computational Biologist > The Informatics Institute at > The University of Medicine & Dentistry of NJ > > Phone: 973-972-5034 > Fax: 973-972-7412 > Email: golharam at umdnj.edu > > > > > Hi all, > I am looking for some tool that enables me to search a (custom) > sequence database using the 'profile' (BLAST generated) of the query > sequence rather than a query sequence itself. If anyone is aware of any > such tool, please let me know. > > Regards, > Raj > From dmb at mrc-dunn.cam.ac.uk Thu Sep 9 10:43:31 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Thu, 9 Sep 2004 15:43:31 +0100 (BST) Subject: [BiO BB] Search a Profile against a sequence database In-Reply-To: <33e68eb104090907256d114b23@mail.gmail.com> Message-ID: On Thu, 9 Sep 2004, Raj wrote: >Golhar, > I need a gapless alignment. PSIBLAST does not have a gapless >alignment option. Thanks for the answer though. Do you mean global alignment? SAM and HMMER both have a 'global global' option (I think) for HMM to sequence alignment. You can find tools to convert a psiblast profile into a HMM. Don't have the details right now though. > >Regards, >Raj > > >On Wed, 8 Sep 2004 17:27:43 -0400, Ryan Golhar wrote: >> You can use PSI-BLAST. Generate your sequence database using formatdb >> from the NCBI toolkit, and then use PSI-BLAST to search your custom >> database using your profile... >> >> ----- >> Ryan Golhar >> Computational Biologist >> The Informatics Institute at >> The University of Medicine & Dentistry of NJ >> >> Phone: 973-972-5034 >> Fax: 973-972-7412 >> Email: golharam at umdnj.edu >> >> >> > >> >> Hi all, >> I am looking for some tool that enables me to search a (custom) >> sequence database using the 'profile' (BLAST generated) of the query >> sequence rather than a query sequence itself. If anyone is aware of any >> such tool, please let me know. >> >> Regards, >> Raj >> >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From merin at macfast.org Thu Sep 9 10:50:20 2004 From: merin at macfast.org (merin) Date: 9 Sep 2004 14:50:20 -0000 Subject: [BiO BB] Ramachandran plot Message-ID: <20040909145020.25674.qmail@macfast.org> Hello all, Can you please help me? I'm very much interested in Ramachandran plot. I searched a lot for information relating to its applications,but got very little information. Can you please help me in this regard? 1)What are the important applications of Ramachandran plot in structural Bioinformatics? 2)If you change an amino acid in the protein sequence,what precise effect does it have on the plot and what are the applications in this regard? 3)Does it have any application in Homology modelling? merin From pfern at igc.gulbenkian.pt Thu Sep 9 11:11:28 2004 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Thu, 9 Sep 2004 16:11:28 +0100 Subject: [BiO BB] Ramachandran plot References: <20040909145020.25674.qmail@macfast.org> Message-ID: <016f01c4967f$47d39c80$962016ac@biocasept> Hello Merin Did you have a look at free online course materials? for example at: http://www.cryst.bbk.ac.uk/PPS2/course/section3/rama.html or http://www.cgl.ucsf.edu/home/glasfeld/tutorial/AAA/AAA.html http://bmbiris.bmb.uga.edu/wampler/tutorial/prot2.html Best of luck Pedro Fernandes ----- Original Message ----- From: "merin" To: Sent: Thursday, September 09, 2004 3:50 PM Subject: [BiO BB] Ramachandran plot > Hello all, > Can you please help me? > I'm very much interested in Ramachandran plot. > I searched a lot for information relating to its applications,but got > very little information. > Can you please help me in this regard? > 1)What are the important applications of Ramachandran plot in structural > Bioinformatics? > 2)If you change an amino acid in the protein sequence,what precise > effect does it have on the plot and what are the applications in this > regard? > 3)Does it have any application in Homology modelling? > > merin > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From pankaj at nii.res.in Wed Sep 15 04:40:58 2004 From: pankaj at nii.res.in (Pankaj) Date: Wed, 15 Sep 2004 14:10:58 +0530 (IST) Subject: [BiO BB] (no subject) Message-ID: Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar From pankaj at nii.res.in Wed Sep 15 04:57:29 2004 From: pankaj at nii.res.in (Pankaj) Date: Wed, 15 Sep 2004 14:27:29 +0530 (IST) Subject: [BiO BB] rmsd calculation Message-ID: Hi all, I have a pdb file of 2 superimposed structures. I want to know the rmsd of a part of 1 structure to a part of the 2 structure. For this rmsd calculation I dont want to disturb the superimposition. how do I do that? thanking all in advance Pankaj Kamra Research Scholar From C.Pettitt at cs.ucl.ac.uk Wed Sep 15 06:22:24 2004 From: C.Pettitt at cs.ucl.ac.uk (Chris Pettitt) Date: Wed, 15 Sep 2004 11:22:24 +0100 Subject: [BiO BB] (no subject) In-Reply-To: References: Message-ID: <1095243744.5110.0.camel@opsin.cs.ucl.ac.uk> Try this: http://acrmwww.biochem.ucl.ac.uk/software/profit/ On Wed, 2004-09-15 at 09:40, Pankaj wrote: > Hi all, > I have a pdb file of 2 superimposed structures. I want to know the > rmsd of a part of 1 structure to a part of the 2 structure. For this > rmsd calculation I dont want to disturb the superimposition. how do I > do that? > thanking all in advance > Pankaj Kamra > Research Scholar > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From jon.rees at bioinformaticsforumuk.net Tue Sep 7 09:26:02 2004 From: jon.rees at bioinformaticsforumuk.net (Jon Rees) Date: Tue, 7 Sep 2004 14:26:02 +0100 Subject: [BiO BB] Young Bioinformatics Forum 2004 - Free Registration and 2nd Call for Posters Message-ID: <0b4801c494de$38748f30$268449a1@acs.brookes.ac.uk> **************************************************************************** Young Bioinformatics Forum 2004 - Free Registration and 2nd Call for Posters http://www.ybf.org/ -- FREE REGISTRATION -- Note: Change of Date to 20th Oct **************************************************************************** The 2nd Young Bioinformaticians' Forum will take place in Oxford, UK on Wednesday October 20th 2004 at the prestigious Said Business School. YBF is organised by the Royal Society of Chemistry Molecular Modelling Group and the Oxford Bioinformatics Forum. The program includes competitive oral paper presentations sessions (prize ?250) for the Young Bioinformatician of the Year award with invited talks on areas of Systems Biology, Microarrays and Clustering, Protein Evolution and Interactions. There is also the YBF Poster competition (prize ?100) which is open to new submissions until October 10th, 2004. Many abstracts are already available online at http://ybf.org/cgi-bin/show_abstracts.cgi There is no early registration deadline but there are a limited number of places so do register soon. Delegates such as interested PhD students, post-docs and more senior scientists who work in bioinformatics and related fields such as molecular biology are welcome to attend as spectators. Please visit the meeting web site at http://www.ybf.org or register free of charge at http://ybf.org/registration.htm The meeting also provides a forum for academic researchers and industry innovators to network and make contacts. Proceedings of the meeting will be available online. The purpose of these meetings is to raise awareness of the growing importance of bioinformatics in all areas of biomedical research, both pure and applied, and to provide a forum for young researchers to present their latest research to an audience of peers and potential employers, both academic and industrial. Meetings draw many PhD level bioinformaticians from a wide area of bioinformatics, including contributions in the areas of sequence analysis, structural bioinformatics, and algorithm development. You are encouraged to to pass on this email to your friends and colleagues. If you have any questions or wish to register offline, please contact us: Dr Jon Rees (Project Manager) Oxford Bioinformatics Forum Oxford Brookes University Headington Campus, Gipsy Lane Oxford OX3 0BP United Kingdom Email: ybf(at)bioinformaticsforumuk.net Tel. +44 (0) 1865 484224 Mob. +44 (0) 7970 893371 Fax. +44 (0) 1865 484478 -------------- next part -------------- An HTML attachment was scrubbed... URL: From chea at niaid.nih.gov Wed Sep 15 10:33:14 2004 From: chea at niaid.nih.gov (Anney Che) Date: Wed, 15 Sep 2004 10:33:14 -0400 Subject: [BiO BB] Blast query Message-ID: Hi, Does anyone know how I can set a filter for a blast search? Anney From letondal at pasteur.fr Thu Sep 16 03:51:53 2004 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 16 Sep 2004 09:51:53 +0200 Subject: [BiO BB] Course in informatics for biology 2005, Institut Pasteur Message-ID: <200409160751.i8G7prXT088244@electre.pasteur.fr> Course in informatics for biology 2005 at Institut Pasteur In the series of courses offered at the Pasteur Institute, a course will be offered in informatics in biology. The next session will take place from January to end of April 2005. The main goal of this course is to provide researchers in biology an initial exposure to informatics. Admitance in the course is reserved for those with a degree in biology or a related discipline. With more and more bioinformatics tools available, it becomes increasingly important for researchers in biology to be able both to manage their data, implement their ideas, and judge for themselves the usefulness of new algorithms and software. This course will emphasize fundamental aspects of computer science and apply them to biological examples. Theoretical aspects (algorithm development, logic, problem modeling and design methods), and technical applications (databases and web technologies) that are relevant for biologists will be thoroughly discussed. Programming is presented through the object-oriented paradigm, using a modern high-level language, Python, provided with tools for biology and enabling both prototyping or scripting and the building of important software systems. Learning of additional languages (perl and C) will be available for interested students. Learning during the course will be reinforced with computing exercises, and effective training will be provided by a 2 month research project. The working language of the course is French. For further information, please consult: http://www.pasteur.fr/formation/infobio-en.html Sincerely, -- Catherine Letondal -- Pasteur Institute Computing Center From sajan_lalp at yahoo.co.in Fri Sep 17 07:54:08 2004 From: sajan_lalp at yahoo.co.in (sajan lal) Date: Fri, 17 Sep 2004 12:54:08 +0100 (BST) Subject: [BiO BB] TBS1104 Message-ID: <20040917115408.82346.qmail@web8310.mail.in.yahoo.com> subject,TBS1104 Sir, Please find my updated resume for your kind consideration .My expected salary is 2 lace per year and you can call on this (Phone: 022-34489957 )Any time Regards Sajanlal.. ====================================================== Sajan lal P M-7/7,Bhanumathi Hsg.socy.Ltd . Bamgur Nagar,Goregaon(w) Email : sajan_lalp at yahoo.co.in/ sajanlal at india.com Phone: 022-34489957 Any time (M),Mumbai 59 ________________________________________________________________________ Objective: To work in a congenial environment and utilize my Biotechnological skills for development of need based technologies Work experience 1) Worked as a Q.C At U.E.C Andheri for 8 months (it is B.I.S Approved packaged drinking water company where I had bee per formed 51 Chemical test as well as Micro biology test .) 2) From January 2004-till Date Global Enterprise Infotech Solution, Mumbai & Pune (Technical consultant, Bioinformatics) Job profile: q Genome analysis (data mining ) q Research work conducted on Protein modeling q Corporate training Educational Qualifications M.Sc. Biotechnology First class2002 (Subjects: Biochemistry and Biophysics,Molecular Genetics,Microbiology and Immunology,Molecular and Developmental Biology Enzymology and Enzyme technology,Plant Molecular Biology,Plant Biotechnology,Genetic Engineering,Bioprocess technology,Animal Biotechnology,Recombinant DNA technology,Industrial Biotechnology Immunotechnology,Biostatistics and Bioinformatics) PROJECT AND RESEARCH EXPERIENCE project work upon 'Solid Culturing of aspergillus niger production of glucoamylase' Periyar University, Tamilnadu B.Sc Zoology,Chemistry, Botany First class 1997 M.G University, Kerala V.H.S.E second class Bord Of Vocational Higher Secondary Education Kerala Computer Knowledge a) Language: C and PERL, b)Windows, NT, DOS and Linux operating systems. Bioinformatics tools and packages worked upon Proteomics, Genomics, Bioinformatics, Molecular Modeling & Drug design Tools / packages used : EMBOSS, BLAST, FASTA, Clustal X/W, Phylodraw, PHYLIP, Modeller, Swiss-PDBViewer, Cn3d, PROCHECK, Chromas, Genalysis, Rasmol, RasTop, ISIS -draw, Vector NTI, Hyperchem, Chem-SW. NCBI, EMBL, and PDB databases, , SEMINARS, CONFERENCES AND WORKSHOPS ATTENDED 1)Seminar on 'Current developments in Human Genome Project' conducted by Dept. of Biotechnology Bharathidasan University on 09-11 march 2001, Tamilnadu, India 2)National level seminar on 'Current trends and future direction in Life science' organized by Flora, 4-5 January 2002, Tamilnadu, India 3)A workshop on 'Training on Plant Tissue Culture' conducted by Centre for Biodiversity and Biotechnology, 26-31 December 2000, Tamilnadu, India 4)Workshop on 'Basic techniques in Molecular Biology' organized by Dept. of Biotechnology, MCAS, 3rd march, Tamilnadu, India Personal Information Corresponding Address : M-7/7,Bhanumathi Hsg.socy.Ltd . Email Bamgur Nagar,Goregaon(w) : sajan_lalp at yahoo.co.in/ sajanlal at india.com Date of birth : 21-04-1976 Sex :Male Marital status :Single Nationality :Indian Languages known :English, Hindi,Malayalam,Tamil Yahoo! India Matrimony: Find your life partneronline. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sariego9 at yahoo.com Fri Sep 17 10:44:49 2004 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 17 Sep 2004 07:44:49 -0700 (PDT) Subject: [BiO BB] SWDA Message-ID: <20040917144449.11454.qmail@web14305.mail.yahoo.com> Hello all, I am searching for an implementation of the Smith-Waterman algorythm, but with the double-affine gapping that is publicly available. I know FASTA has a full SW implementation, but it does not offer the second gap penalty score option. I also am aware that Paracel and DeCypher both have these, but they are far from free. Any help would be appreciated. Thanks. Diego __________________________________ Do you Yahoo!? Yahoo! Mail - 50x more storage than other providers! http://promotions.yahoo.com/new_mail From enoumen at rsvs.ulaval.ca Fri Sep 17 10:49:51 2004 From: enoumen at rsvs.ulaval.ca (Etienne Noumen) Date: Fri, 17 Sep 2004 10:49:51 -0400 Subject: [BiO BB] SWDA References: <20040917144449.11454.qmail@web14305.mail.yahoo.com> Message-ID: <001101c49cc5$965a09b0$8b59cb84@sbf.ulaval.ca> Oui, je trouve tjrs 0 pour VI. J'ai meme verifie manuellement ds le fichier resultat avec Ctrl KF et j'en ai pas trouv?. ----- Original Message ----- From: "Diego Martinez" To: Sent: Friday, September 17, 2004 10:44 AM Subject: [BiO BB] SWDA > Hello all, > > I am searching for an implementation of the Smith-Waterman > algorythm, but with the double-affine gapping that is > publicly available. I know FASTA has a full SW implementation, > but it does not offer the second gap penalty score option. > I also am aware that Paracel and DeCypher both have these, > but they are far from free. Any help would be > appreciated. > > Thanks. > > Diego > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - 50x more storage than other providers! > http://promotions.yahoo.com/new_mail > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From enoumen at rsvs.ulaval.ca Fri Sep 17 10:50:50 2004 From: enoumen at rsvs.ulaval.ca (Etienne Noumen) Date: Fri, 17 Sep 2004 10:50:50 -0400 Subject: [BiO BB] SWDA References: <20040917144449.11454.qmail@web14305.mail.yahoo.com> Message-ID: <001901c49cc5$b9197440$8b59cb84@sbf.ulaval.ca> please. excuse me for my last message in french, it was not meant for the list. Thank you etienne ----- Original Message ----- From: "Diego Martinez" To: Sent: Friday, September 17, 2004 10:44 AM Subject: [BiO BB] SWDA > Hello all, > > I am searching for an implementation of the Smith-Waterman > algorythm, but with the double-affine gapping that is > publicly available. I know FASTA has a full SW implementation, > but it does not offer the second gap penalty score option. > I also am aware that Paracel and DeCypher both have these, > but they are far from free. Any help would be > appreciated. > > Thanks. > > Diego > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - 50x more storage than other providers! > http://promotions.yahoo.com/new_mail > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From mgollery at unr.edu Fri Sep 17 12:59:06 2004 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 17 Sep 2004 09:59:06 -0700 Subject: [BiO BB] SWDA In-Reply-To: <20040917144449.11454.qmail@web14305.mail.yahoo.com> References: <20040917144449.11454.qmail@web14305.mail.yahoo.com> Message-ID: <414B17DA.5040201@unr.edu> Hi Diego, I looked for this a couple of years ago whilst working on it for the DeCypher. There was nothing at the time, but this might have changed. I certainly like the double-affine scoring, so if there is no publicly available implementation, somebody ought to get to work on it! Marty Diego Martinez wrote: > Hello all, > > I am searching for an implementation of the Smith-Waterman > algorythm, but with the double-affine gapping that is > publicly available. I know FASTA has a full SW implementation, > but it does not offer the second gap penalty score option. > I also am aware that Paracel and DeCypher both have these, > but they are far from free. Any help would be > appreciated. > > Thanks. > > Diego > > > > __________________________________ > Do you Yahoo!? > Yahoo! Mail - 50x more storage than other providers! > http://promotions.yahoo.com/new_mail > _______________________________________________ > 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 ----------- Marty's Law- the number of Bioinformatics acronyms will double every 18 months. From dmb at mrc-dunn.cam.ac.uk Fri Sep 17 13:19:17 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 17 Sep 2004 18:19:17 +0100 (BST) Subject: [BiO BB] SWDA In-Reply-To: <414B17DA.5040201@unr.edu> Message-ID: On Fri, 17 Sep 2004, Martin Gollery wrote: >Hi Diego, > >I looked for this a couple of years ago whilst working on it for the >DeCypher. There was nothing at the time, but this might have changed. I >certainly like the double-affine scoring, so if there is no publicly >available implementation, somebody ought to get to work on it! Can it be done in perl? I think such an implementation could be very usefull for teaching bioinformatics. > >Marty > >Diego Martinez wrote: >> Hello all, >> >> I am searching for an implementation of the Smith-Waterman >> algorythm, but with the double-affine gapping that is >> publicly available. I know FASTA has a full SW implementation, >> but it does not offer the second gap penalty score option. >> I also am aware that Paracel and DeCypher both have these, >> but they are far from free. Any help would be >> appreciated. >> >> Thanks. >> >> Diego >> >> >> >> __________________________________ >> Do you Yahoo!? >> Yahoo! Mail - 50x more storage than other providers! >> http://promotions.yahoo.com/new_mail >> _______________________________________________ >> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >> https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From mgollery at unr.edu Fri Sep 17 13:31:12 2004 From: mgollery at unr.edu (Martin Gollery) Date: Fri, 17 Sep 2004 10:31:12 -0700 Subject: [BiO BB] SWDA In-Reply-To: References: Message-ID: <414B1F60.2060802@unr.edu> Yes, but it would be painfully slow! Marty Dan Bolser wrote: > On Fri, 17 Sep 2004, Martin Gollery wrote: > > >>Hi Diego, >> >>I looked for this a couple of years ago whilst working on it for the >>DeCypher. There was nothing at the time, but this might have changed. I >>certainly like the double-affine scoring, so if there is no publicly >>available implementation, somebody ought to get to work on it! > > > Can it be done in perl? > > I think such an implementation could be very usefull for teaching > bioinformatics. > > > >>Marty >> >>Diego Martinez wrote: >> >>>Hello all, >>> >>>I am searching for an implementation of the Smith-Waterman >>>algorythm, but with the double-affine gapping that is >>>publicly available. I know FASTA has a full SW implementation, >>>but it does not offer the second gap penalty score option. >>>I also am aware that Paracel and DeCypher both have these, >>>but they are far from free. Any help would be >>>appreciated. >>> >>>Thanks. >>> >>>Diego >>> >>> >>> >>>__________________________________ >>>Do you Yahoo!? >>>Yahoo! Mail - 50x more storage than other providers! >>>http://promotions.yahoo.com/new_mail >>>_______________________________________________ >>>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 ----------- Marty's Law- the number of Bioinformatics acronyms will double every 18 months. From dmb at mrc-dunn.cam.ac.uk Fri Sep 17 13:55:41 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 17 Sep 2004 18:55:41 +0100 (BST) Subject: [BiO BB] SWDA In-Reply-To: <414B1F60.2060802@unr.edu> Message-ID: On Fri, 17 Sep 2004, Martin Gollery wrote: >Yes, but it would be painfully slow! >Marty Even over two sequences? > >Dan Bolser wrote: > >> On Fri, 17 Sep 2004, Martin Gollery wrote: >> >> >>>Hi Diego, >>> >>>I looked for this a couple of years ago whilst working on it for the >>>DeCypher. There was nothing at the time, but this might have changed. I >>>certainly like the double-affine scoring, so if there is no publicly >>>available implementation, somebody ought to get to work on it! >> >> >> Can it be done in perl? >> >> I think such an implementation could be very usefull for teaching >> bioinformatics. >> >> >> >>>Marty >>> >>>Diego Martinez wrote: >>> >>>>Hello all, >>>> >>>>I am searching for an implementation of the Smith-Waterman >>>>algorythm, but with the double-affine gapping that is >>>>publicly available. I know FASTA has a full SW implementation, >>>>but it does not offer the second gap penalty score option. >>>>I also am aware that Paracel and DeCypher both have these, >>>>but they are far from free. Any help would be >>>>appreciated. >>>> >>>>Thanks. >>>> >>>>Diego >>>> >>>> >>>> >>>>__________________________________ >>>>Do you Yahoo!? >>>>Yahoo! Mail - 50x more storage than other providers! >>>>http://promotions.yahoo.com/new_mail >>>>_______________________________________________ >>>>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 ryangolhar at hotmail.com Fri Sep 17 14:04:19 2004 From: ryangolhar at hotmail.com (Ryan Golhar) Date: Fri, 17 Sep 2004 14:04:19 -0400 Subject: [BiO BB] SWDA In-Reply-To: Message-ID: <003801c49ce0$c0b744a0$4722db82@GOLHARMOBILE1> And why would you want to use a double-affine scoring scheme? What benefits does it have? Ryan -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Dan Bolser Sent: Friday, September 17, 2004 1:56 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] SWDA On Fri, 17 Sep 2004, Martin Gollery wrote: >Yes, but it would be painfully slow! >Marty Even over two sequences? > >Dan Bolser wrote: > >> On Fri, 17 Sep 2004, Martin Gollery wrote: >> >> >>>Hi Diego, >>> >>>I looked for this a couple of years ago whilst working on it for the >>>DeCypher. There was nothing at the time, but this might have changed. I >>>certainly like the double-affine scoring, so if there is no publicly >>>available implementation, somebody ought to get to work on it! >> >> >> Can it be done in perl? >> >> I think such an implementation could be very usefull for teaching >> bioinformatics. >> >> >> >>>Marty >>> >>>Diego Martinez wrote: >>> >>>>Hello all, >>>> >>>>I am searching for an implementation of the Smith-Waterman >>>>algorythm, but with the double-affine gapping that is publicly >>>>available. I know FASTA has a full SW implementation, but it does >>>>not offer the second gap penalty score option. I also am aware that >>>>Paracel and DeCypher both have these, but they are far from free. >>>>Any help would be appreciated. >>>> >>>>Thanks. >>>> >>>>Diego >>>> >>>> >>>> >>>>__________________________________ >>>>Do you Yahoo!? >>>>Yahoo! Mail - 50x more storage than other providers! >>>>http://promotions.yahoo.com/new_mail >>>>_______________________________________________ >>>>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 > > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sariego9 at yahoo.com Fri Sep 17 14:42:25 2004 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 17 Sep 2004 11:42:25 -0700 (PDT) Subject: [BiO BB] SWDA In-Reply-To: Message-ID: <20040917184225.18510.qmail@web14323.mail.yahoo.com> I dont think it would be so slow on a couple of sequences, I just dont know how to do recursion.I mean, SW is already like 50 X slower than a banded implementation. Diego --- Dan Bolser wrote: > On Fri, 17 Sep 2004, Martin Gollery wrote: > > >Yes, but it would be painfully slow! > >Marty > > Even over two sequences? > > > > > > > >Dan Bolser wrote: > > > >> On Fri, 17 Sep 2004, Martin Gollery wrote: > >> > >> > >>>Hi Diego, > >>> > >>>I looked for this a couple of years ago whilst working on it for the > >>>DeCypher. There was nothing at the time, but this might have changed. I > >>>certainly like the double-affine scoring, so if there is no publicly > >>>available implementation, somebody ought to get to work on it! > >> > >> > >> Can it be done in perl? > >> > >> I think such an implementation could be very usefull for teaching > >> bioinformatics. > >> > >> > >> > >>>Marty > >>> > >>>Diego Martinez wrote: > >>> > >>>>Hello all, > >>>> > >>>>I am searching for an implementation of the Smith-Waterman > >>>>algorythm, but with the double-affine gapping that is > >>>>publicly available. I know FASTA has a full SW implementation, > >>>>but it does not offer the second gap penalty score option. > >>>>I also am aware that Paracel and DeCypher both have these, > >>>>but they are far from free. Any help would be > >>>>appreciated. > >>>> > >>>>Thanks. > >>>> > >>>>Diego > >>>> > >>>> > >>>> > >>>>__________________________________ > >>>>Do you Yahoo!? > >>>>Yahoo! Mail - 50x more storage than other providers! > >>>>http://promotions.yahoo.com/new_mail > >>>>_______________________________________________ > >>>>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 > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From sariego9 at yahoo.com Fri Sep 17 14:44:32 2004 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 17 Sep 2004 11:44:32 -0700 (PDT) Subject: [BiO BB] SWDA In-Reply-To: <003801c49ce0$c0b744a0$4722db82@GOLHARMOBILE1> Message-ID: <20040917184432.63011.qmail@web14301.mail.yahoo.com> Double Affine has two gap extension scores, the second implemented after a specified number of mismatches. you get a longer, more accurate alignment than BLASTP, I mean that as it iddentifies more AA's in common. I deal with very distant proteins most often. Diego --- Ryan Golhar wrote: > And why would you want to use a double-affine scoring scheme? What > benefits does it have? > > Ryan > > > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Dan > Bolser > Sent: Friday, September 17, 2004 1:56 PM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] SWDA > > > On Fri, 17 Sep 2004, Martin Gollery wrote: > > >Yes, but it would be painfully slow! > >Marty > > Even over two sequences? > > > > > > > >Dan Bolser wrote: > > > >> On Fri, 17 Sep 2004, Martin Gollery wrote: > >> > >> > >>>Hi Diego, > >>> > >>>I looked for this a couple of years ago whilst working on it for the > >>>DeCypher. There was nothing at the time, but this might have changed. > I > >>>certainly like the double-affine scoring, so if there is no publicly > >>>available implementation, somebody ought to get to work on it! > >> > >> > >> Can it be done in perl? > >> > >> I think such an implementation could be very usefull for teaching > >> bioinformatics. > >> > >> > >> > >>>Marty > >>> > >>>Diego Martinez wrote: > >>> > >>>>Hello all, > >>>> > >>>>I am searching for an implementation of the Smith-Waterman > >>>>algorythm, but with the double-affine gapping that is publicly > >>>>available. I know FASTA has a full SW implementation, but it does > >>>>not offer the second gap penalty score option. I also am aware that > >>>>Paracel and DeCypher both have these, but they are far from free. > >>>>Any help would be appreciated. > >>>> > >>>>Thanks. > >>>> > >>>>Diego > >>>> > >>>> > >>>> > >>>>__________________________________ > >>>>Do you Yahoo!? > >>>>Yahoo! Mail - 50x more storage than other providers! > >>>>http://promotions.yahoo.com/new_mail > >>>>_______________________________________________ > >>>>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 > > > > > > _______________________________________________ > 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 > ===== ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From ryangolhar at hotmail.com Fri Sep 17 15:01:52 2004 From: ryangolhar at hotmail.com (Ryan Golhar) Date: Fri, 17 Sep 2004 15:01:52 -0400 Subject: [BiO BB] SWDA In-Reply-To: <20040917184225.18510.qmail@web14323.mail.yahoo.com> Message-ID: <000001c49ce8$cae00040$4200a8c0@GOLHARMOBILE1> I did a java implementation of Smith-Waterman long ago and it was incorporated into Jaligner. The source code is available at http://sourceforge.net/projects/jaligner. The code has been reworked -- looks much more complicated than what I initially wrote. That should get you started. As for speed, it wasn't slow, it worked very well... ----- Ryan Golhar Computational Biologist The Informatics Institute at The University of Medicine & Dentistry of NJ Phone: 973-972-5034 Fax: 973-972-7412 Email: golharam at umdnj.edu -----Original Message----- From: bio_bulletin_board-admin at bioinformatics.org [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Diego Martinez Sent: Friday, September 17, 2004 2:42 PM To: bio_bulletin_board at bioinformatics.org Subject: Re: [BiO BB] SWDA I dont think it would be so slow on a couple of sequences, I just dont know how to do recursion.I mean, SW is already like 50 X slower than a banded implementation. Diego --- Dan Bolser wrote: > On Fri, 17 Sep 2004, Martin Gollery wrote: > > >Yes, but it would be painfully slow! > >Marty > > Even over two sequences? > > > > > > > >Dan Bolser wrote: > > > >> On Fri, 17 Sep 2004, Martin Gollery wrote: > >> > >> > >>>Hi Diego, > >>> > >>>I looked for this a couple of years ago whilst working on it for > >>>the > >>>DeCypher. There was nothing at the time, but this might have changed. I > >>>certainly like the double-affine scoring, so if there is no publicly > >>>available implementation, somebody ought to get to work on it! > >> > >> > >> Can it be done in perl? > >> > >> I think such an implementation could be very usefull for teaching > >> bioinformatics. > >> > >> > >> > >>>Marty > >>> > >>>Diego Martinez wrote: > >>> > >>>>Hello all, > >>>> > >>>>I am searching for an implementation of the Smith-Waterman > >>>>algorythm, but with the double-affine gapping that is publicly > >>>>available. I know FASTA has a full SW implementation, but it does > >>>>not offer the second gap penalty score option. I also am aware > >>>>that Paracel and DeCypher both have these, but they are far from > >>>>free. Any help would be appreciated. > >>>> > >>>>Thanks. > >>>> > >>>>Diego > >>>> > >>>> > >>>> > >>>>__________________________________ > >>>>Do you Yahoo!? > >>>>Yahoo! Mail - 50x more storage than other providers! > >>>>http://promotions.yahoo.com/new_mail > >>>>_______________________________________________ > >>>>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 > > > > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > ===== ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ~~ .=$=. .=$=. .=$=. .=$=. .=$=. =$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From sariego9 at yahoo.com Fri Sep 17 15:11:14 2004 From: sariego9 at yahoo.com (Diego Martinez) Date: Fri, 17 Sep 2004 12:11:14 -0700 (PDT) Subject: [BiO BB] SWDA In-Reply-To: <000001c49ce8$cae00040$4200a8c0@GOLHARMOBILE1> Message-ID: <20040917191115.58983.qmail@web14324.mail.yahoo.com> thanks Ryan, I will give it a shot. Diego --- Ryan Golhar wrote: > I did a java implementation of Smith-Waterman long ago and it was > incorporated into Jaligner. The source code is available at > http://sourceforge.net/projects/jaligner. The code has been reworked -- > looks much more complicated than what I initially wrote. That should > get you started. As for speed, it wasn't slow, it worked very well... > > > ----- > Ryan Golhar > Computational Biologist > The Informatics Institute at > The University of Medicine & Dentistry of NJ > > Phone: 973-972-5034 > Fax: 973-972-7412 > Email: golharam at umdnj.edu > > -----Original Message----- > From: bio_bulletin_board-admin at bioinformatics.org > [mailto:bio_bulletin_board-admin at bioinformatics.org] On Behalf Of Diego > Martinez > Sent: Friday, September 17, 2004 2:42 PM > To: bio_bulletin_board at bioinformatics.org > Subject: Re: [BiO BB] SWDA > > > I dont think it would be so slow on a couple of > sequences, I just dont know how to do > recursion.I mean, SW is already like > 50 X slower than a banded implementation. > > Diego > > > --- Dan Bolser wrote: > > > On Fri, 17 Sep 2004, Martin Gollery wrote: > > > > >Yes, but it would be painfully slow! > > >Marty > > > > Even over two sequences? > > > > > > > > > > > > > >Dan Bolser wrote: > > > > > >> On Fri, 17 Sep 2004, Martin Gollery wrote: > > >> > > >> > > >>>Hi Diego, > > >>> > > >>>I looked for this a couple of years ago whilst working on it for > > >>>the > > >>>DeCypher. There was nothing at the time, but this might have > changed. I > > >>>certainly like the double-affine scoring, so if there is no > publicly > > >>>available implementation, somebody ought to get to work on it! > > >> > > >> > > >> Can it be done in perl? > > >> > > >> I think such an implementation could be very usefull for teaching > > >> bioinformatics. > > >> > > >> > > >> > > >>>Marty > > >>> > > >>>Diego Martinez wrote: > > >>> > > >>>>Hello all, > > >>>> > > >>>>I am searching for an implementation of the Smith-Waterman > > >>>>algorythm, but with the double-affine gapping that is publicly > > >>>>available. I know FASTA has a full SW implementation, but it does > > > >>>>not offer the second gap penalty score option. I also am aware > > >>>>that Paracel and DeCypher both have these, but they are far from > > >>>>free. Any help would be appreciated. > > >>>> > > >>>>Thanks. > > >>>> > > >>>>Diego > > >>>> > > >>>> > > >>>> > > >>>>__________________________________ > > >>>>Do you Yahoo!? > > >>>>Yahoo! Mail - 50x more storage than other providers! > > >>>>http://promotions.yahoo.com/new_mail > > >>>>_______________________________________________ > > >>>>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 > > > > > > > > > > _______________________________________________ > > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > ===== > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > ~~ > > .=$=. .=$=. .=$=. .=$=. .=$=. > =$=. > @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | > | > | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | > | > | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ > | > ~' `~$~' `~$~' `~$~' `~$~' `~$~' > `~ > > > > _______________________________ > Do you Yahoo!? > Declare Yourself - Register online to vote today! http://vote.yahoo.com > _______________________________________________ > 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 > ===== ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .=$=. .=$=. .=$=. .=$=. .=$=. .=$=. @ @ | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | @ @ | | | | @ | | | @ @ | | | @ | | | @ @ | | | @ | | | @ @ | ~' `~$~' `~$~' `~$~' `~$~' `~$~' `~ _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From sourangshu at csa.iisc.ernet.in Sun Sep 19 11:32:56 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Sun, 19 Sep 2004 21:02:56 +0530 (IST) Subject: [BiO BB] rmsd calculation In-Reply-To: References: Message-ID: Hi Pankaj, I believe you are having problem in finding out the equivalences. Generally, a nearest neighbour approach is very intuitive. That is you say that one residue has been equivalenced with it's nearest spatial neighbour. However, it is not guarranteed to be symmetric. That is, a is NN for b doesn't mean b has to be NN for a. You can use any heuristic there. After this RMSD calculation is just computation !!! Sourangshu On Wed, 15 Sep 2004, Pankaj wrote: > Hi all, > I have a pdb file of 2 superimposed structures. I want to know the > rmsd of a part of 1 structure to a part of the 2 structure. For this > rmsd calculation I dont want to disturb the superimposition. how do I > do that? > thanking all in advance > Pankaj Kamra > Research Scholar > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From sourangshu at csa.iisc.ernet.in Sun Sep 19 12:08:28 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Sun, 19 Sep 2004 21:38:28 +0530 (IST) Subject: [BiO BB] Blast query In-Reply-To: References: Message-ID: Hi Anney, You can check the link : http://cgpdb.ucdavis.edu/BlastParser/Blast_Parser.html You can also type in "Blast Parser" in google and check the other results. Sourangshu -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, IISc, Bangalore. http://people.csa.iisc.ernet.in/sourangshu On Wed, 15 Sep 2004, Anney Che wrote: > Hi, > > Does anyone know how I can set a filter for a blast search? > > Anney > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From ahiresunita at yahoo.com Tue Sep 21 02:10:22 2004 From: ahiresunita at yahoo.com (sunita ahire) Date: Mon, 20 Sep 2004 23:10:22 -0700 (PDT) Subject: [BiO BB] PDB vs MSD In-Reply-To: <20040917115408.82346.qmail@web8310.mail.in.yahoo.com> Message-ID: <20040921061022.66954.qmail@web61004.mail.yahoo.com> Hi, can somebody tell me what are the differences betwwen PDB and MSD from database point of view(other than PDB is flat file and MSD is relational database). Any help is greatly appreciated. Thanx in advance. ~Sunita --------------------------------- Do you Yahoo!? New and Improved Yahoo! Mail - 100MB free storage! -------------- next part -------------- An HTML attachment was scrubbed... URL: From dmb at mrc-dunn.cam.ac.uk Tue Sep 21 04:35:26 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 21 Sep 2004 09:35:26 +0100 (BST) Subject: [BiO BB] PDB vs MSD In-Reply-To: <20040921061022.66954.qmail@web61004.mail.yahoo.com> Message-ID: One benifit of the MSD over the PDB is that it cleans and normalizes the data, making links to secondary structure, taxonomy, uniprot, scop, cath, pfam and ligand databases very easy (to mention a few). Secondly it is built around the concept of a biomolecule, something which is generated over an individual PDB file (which tipically contains only the asymetrical unit in crystallographic terms). Curently you need oracle to get independant access, or they can dump custom queries for you. The API is good, but down last time I checked. Last time I checked not all the data was correctly loaded, although that may have changed. They have a nifty web query form, which you shouldn't confuse with the PQS query pages at the MSD (group) website. PQS is consumed by the MSD database (at the EBI, heh). One criticism is that it is yet another pdb cleanup, including mmDB at the NCBI and mmCIF at the PDB. There is no community consensus on the 'clean' data. i.e. they are all potentially different. I am a DB type person, so I like MSD a lot. I hope the current problems are only teething problems (like where is the mysql version?), and this could become a very powerfull tool for the community. On Mon, 20 Sep 2004, sunita ahire wrote: >Hi, can somebody tell me what are the differences betwwen PDB and MSD >from database point of view(other than PDB is flat file and MSD is >relational database). Any help is greatly appreciated. > >Thanx in advance. > >~Sunita > > > > >--------------------------------- >Do you Yahoo!? >New and Improved Yahoo! Mail - 100MB free storage! From stefanielager at fastmail.ca Tue Sep 21 06:38:28 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Tue, 21 Sep 2004 10:38:28 +0000 (UTC) Subject: [BiO BB] scan_for_matches Message-ID: <20040921103829.2BD49863A29@mail.interchange.ca> Hi, I have problems to compile the scan_for_matches pattern searching program on Linux (gcc 3.4.0). When I try to compile it with "gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c", I get "error:conflicting types for 'malloc'" line 17 in scan_for_matches.c and line 235 in ggpunit.c . Does anyone have a compiled version of scan_for_matches for Linux, or know how to fix the "malloc" problem? Stefanie _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From dig at bioinformatics.org Tue Sep 21 08:59:49 2004 From: dig at bioinformatics.org (Dmitri I GOULIAEV) Date: Tue, 21 Sep 2004 08:59:49 -0400 Subject: [BiO BB] scan_for_matches In-Reply-To: <20040921103829.2BD49863A29@mail.interchange.ca> Message-ID: <20040921125948.GA26889@www.bioinformatics.org> Hi, Stefanie! On Tue, Sep 21, 2004 at 10:38:28AM +0000, Stefanie Lager wrote: > I have problems to compile the scan_for_matches pattern searching > program on Linux (gcc 3.4.0). When I try to compile it with > "gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c", I get > "error:conflicting types for 'malloc'" line 17 in scan_for_matches.c and > line 235 in ggpunit.c . Does anyone have a compiled version of > scan_for_matches for Linux, or know how to fix the "malloc" problem? To fix it, you will need to change the line 235 in ggpunit.c: old: char *malloc(int ln); new: extern void *malloc (size_t ln); And rerun the compiler. Hope this help, -- DIG (Dmitri I GOULIAEV) http://bioinformatics.org/~dig/ 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 -------------- next part -------------- diff -ruN ScanForMatches.O/ggpunit.c ScanForMatches.N/ggpunit.c --- ScanForMatches.O/ggpunit.c 1997-02-20 11:10:25.000000000 -0600 +++ ScanForMatches.N/ggpunit.c 2004-09-21 07:51:15.000000000 -0500 @@ -232,7 +232,7 @@ int cont_match PROTO((char *hits[])); int pattern_match PROTO((punit_t *pu,char *start,char *end,char *hits[],int first, punit_t **BR1)); int collect_hits PROTO((struct punit *pu,char **revhits)); -char *malloc(int ln); +extern void *malloc (size_t ln); /* ============================================================= */ struct state *get_state() From dmb at mrc-dunn.cam.ac.uk Tue Sep 21 16:26:17 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 21 Sep 2004 21:26:17 +0100 (BST) Subject: [BiO BB] [compbio] 23 September seminar (fwd) Message-ID: ---------- Forwarded message ---------- Date: Tue, 21 Sep 2004 20:30:13 +0100 (BST) From: Loredana Lo Conte To: compbio at sanger.ac.uk Subject: [compbio] 23 September seminar Greetings. There will be a seminar on Thursday, 23 September at 11am in the Max Perutz theater at MRC by Dr. Wolfgang Bluhm of the San Diego Supercomputer Center (RCSB consortium). Title: The reengineered RCSB PDB Web site Abstract: The Protein Data Bank (http://www.pdb.org/, PDB) of the Research Collaboratory for Structural Bioinformatics (RCSB) has been reengineering the current RCSB PDB Web site and database. The reengineered site is built on the improved primary data in the curated mmCIF and XML files (see http://www.rcsb.org/pdb/uniformity/ ). Improvements of the reengineered RCSB PDB include: 1) More accurate search results due to improved data in mmCIF and XML files 2) Better navigation and search tools for both structures and Web site content 3) Browsing of structures according to various classifications and ontologies 4) Integrated searching of PubMed abstracts 5) More detailed reports with additional experimental details 6) New visualization options 7) Data access through Web services 8) The ability to run the entire Web site and database on a laptop ("PDB-in-a-Box") All welcome. Loredana Lo Conte From stefanielager at fastmail.ca Wed Sep 22 02:17:52 2004 From: stefanielager at fastmail.ca (Stefanie Lager) Date: Wed, 22 Sep 2004 06:17:52 +0000 (UTC) Subject: [BiO BB] scan_for_matches Message-ID: <20040922061753.3278986104B@mail.interchange.ca> Thank you Dmitri, Changing line 235 in ggpunit.c according to your instructions, together with modifications of line 240 and 767 in ggpunit.c and line 17 in scan_for_matches.c according to: old: char *malloc(); new: extern void *malloc(); Solved the problems, now it compiled on Linux with gcc, very nice! Stefanie > Hi, Stefanie! > > On Tue, Sep 21, 2004 at 10:38:28AM +0000, Stefanie Lager wrote: > >> I have problems to compile the scan_for_matches pattern searching >> program on Linux (gcc 3.4.0). When I try to compile it with >> "gcc -O -o scan_for_matches ggpunit.c scan_for_matches.c", I get >> "error:conflicting types for 'malloc'" line 17 in scan_for_matches.c >> and line 235 in ggpunit.c . Does anyone have a compiled version of >> scan_for_matches for Linux, or know how to fix the "malloc" problem? > > To fix it, you will need to change the line 235 in ggpunit.c: > > old: char *malloc(int ln); > new: extern void *malloc (size_t ln); > > And rerun the compiler. > > > Hope this help, > _________________________________________________________________ http://fastmail.ca/ - Fast Secure Web Email for Canadians From dig at bioinformatics.org Wed Sep 22 03:46:07 2004 From: dig at bioinformatics.org (Dmitri I GOULIAEV) Date: Wed, 22 Sep 2004 03:46:07 -0400 Subject: [BiO BB] scan_for_matches In-Reply-To: <20040922061753.3278986104B@mail.interchange.ca> Message-ID: <20040922074607.GA22865@www.bioinformatics.org> Hi, Stefanie! On Wed, Sep 22, 2004 at 06:17:52AM +0000, Stefanie Lager wrote: > Thank you Dmitri, You are welcome! > Changing line 235 in ggpunit.c according to your instructions, together > with modifications of line 240 and 767 in ggpunit.c and line 17 in ^^^-(1) ^^^-(2) ^^-(3) [...] I think you can drop them (1,2,3) completely -- the program will compile nicely. Just do not try to compile it with ``-Wall'' option -- or you will have 2 something pages of warnings. Are you going to file the bug report? Best regards, -- DIG (Dmitri I GOULIAEV) http://bioinformatics.org/~dig/ 1024D/63A6C649: 26A0 E4D5 AB3F C2D4 0112 66CD 4343 C0AF 63A6 C649 From jareyes at utalca.cl Wed Sep 22 06:54:53 2004 From: jareyes at utalca.cl (jareyes at utalca.cl) Date: Wed, 22 Sep 2004 06:54:53 -0400 Subject: [BiO BB] Bionformatics and System Biology Message-ID: <1095850493.415159fd8686c@utalca.cl> Hi, I am looking for information about the differences and similarities between Bioinformatics and System Biology. Do you know were can I found some papers, documents or other sources of information about this? Thanks in advanced for yours comments. Jos? Antonio ------------------------------------------------- Este mensaje fue enviado por: http://utalca.cl From jrs at farviolet.com Wed Sep 22 12:35:21 2004 From: jrs at farviolet.com (Jeremy Semeiks) Date: Wed, 22 Sep 2004 09:35:21 -0700 Subject: [BiO BB] Bionformatics and System Biology In-Reply-To: <1095850493.415159fd8686c@utalca.cl> References: <1095850493.415159fd8686c@utalca.cl> Message-ID: <20040922163521.GH317@farviolet.farviolet.com> On Wed, Sep 22, 2004 at 06:54:53AM -0400, jareyes at utalca.cl wrote: > > Hi, I am looking for information about the differences and similarities > between Bioinformatics and System Biology. > Do you know were can I found some papers, documents or other sources of > information about this? > > Thanks in advanced for yours comments. Hi Jose, Check out the FAQ: http://bioinformatics.org/faq/#definitions HTH, Jeremy From forward at hongyu.org Wed Sep 22 12:54:47 2004 From: forward at hongyu.org (Hongyu Zhang) Date: Wed, 22 Sep 2004 09:54:47 -0700 Subject: [BiO BB] BLAST database lock Message-ID: <1095872087.4151ae57d6da3@hongyu.org> Dear all, This is a question on database locking techniques. Here is my situation: I need to run BLAST against NR and NT regularly, but both databases are under regular updates from NCBI website every weekend using a cron job. To avoid running against a half updated copy of NR/NT, usually I will make a separated copy of NR/NT if my job will be running throughout the weekend, but obviously it is a hassle for me to remember to do that every time. Therefore, I am looking for a database locking technique, which could make the whole procedure less cumbersome. I would appreciate hearing from you on what kind of locking mechanisms you are using. Thanks! -- Hongyu Zhang Computational biologist Ceres Inc. From sofia at substancia.com Wed Sep 22 13:47:35 2004 From: sofia at substancia.com (Ana Sofia Figueiredo) Date: Wed, 22 Sep 2004 18:47:35 +0100 Subject: [BiO BB] Bionformatics and System Biology In-Reply-To: <1095850493.415159fd8686c@utalca.cl> References: <1095850493.415159fd8686c@utalca.cl> Message-ID: <200409221847.35261.sofia@substancia.com> Hi, As there is no consensus definition for Systems Biology nor for Bioinformatics, pointing out the differences and similarities amongst them is not straight forward. In my opinion, Systems Biology aims at understanding a biological system (for instace, a cell) as a whole. Instead of looking at the individual elements that constitute a cell, it studies how genes and proteins interact; how fluxes distribute in a metabolic pathway (and why); how does the system reacts to external perturbations, and tries to identify the mechanisms underlying the different phenomena. Then, this information will be used to construct mathematical models. The application of systems theory to biolgy is not new. Authors such as Bertalanffy, Robert Rosen, Savageau have described mathematically biological phenomena, based on engineering principles. Systems biology from those days differs from todays due to the huges amounts of information generated by disciplines as genomics, proteomics and metabolomics. This boom of information is generated by bioinformatics tools. Bioinformatics is the field of intersection between biology and computer sciences. It uses the power of computer sciences to store, analyse, integrate and visualise biological data, in order to answer biologists questions. These papers give a global perspective of systems biology: 1. Kitano H,Computational System Biology Nature (2002) 420; 206-210. 2. Kitano H, Systems Biology: A Brief Overview Science (2002) 295; 1662-1664. 3. Wolkenhauer O, Systems Biology: The reincarnation of systems theory applied to Biology? Briefings in Bioinformatics (2001) Vol. 2 No. 3 258-270. I hope this helps! Sofia On Wednesday 22 September 2004 11:54, jareyes at utalca.cl wrote: > Hi, I am looking for information about the differences and similarities > between Bioinformatics and System Biology. > Do you know were can I found some papers, documents or other sources of > information about this? > > Thanks in advanced for yours comments. > > Jos? Antonio > > > ------------------------------------------------- > Este mensaje fue enviado por: http://utalca.cl > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From cwoelk at popmail.ucsd.edu Thu Sep 16 21:26:34 2004 From: cwoelk at popmail.ucsd.edu (Christopher Woelk) Date: Thu, 16 Sep 2004 18:26:34 -0700 Subject: [BiO BB] Bio::Factory::EMBOSS problem Message-ID: <9CF48CF2-0848-11D9-A05D-00039386AC2E@popmail.ucsd.edu> I was looking for some help I am under OS X 10.3.5 and I have bioperl-1.4 and EMBOSS-2.9.0 installed. I am trying to implement to following code: use Bio::Factory::EMBOSS; # get an EMBOSS application object from the EMBOSS factory $factory = new Bio::Factory::EMBOSS; $application = $factory->program('sixpack'); # run the application with an optional hash containing parameters %input = ( -sequence => $seqobj ); $application->run(\%input); I get the error message: Can't locate Bio/Factory/EMBOSS.pm in @INC (@INC contains: /System/Library/Perl/5.8.1/darwin-thread-multi-2level /System/Library/Perl/5.8.1 /Library/Perl/5.8.1/darwin-thread-multi-2level /Library/Perl/5.8.1 /Library/Perl /Network/Library/Perl/5.8.1/darwin-thread-multi-2level /Network/Library/Perl/5.8.1 /Network/Library/Perl .) at ./iterate_seqs.1.pl line 9. I noticed that EMBOSS.pm does not exist in my Factory directory. I then tried switching to emboss.pm in the AlignIO directory: use Bio::AlignIO::emboss; But got this error message Can't locate object method "program" via package "Bio::AlignIO::emboss" at ./iterate_seqs.1.pl line 40, line 1. Thanks for any help Christopher Woelk, PhD University California at San Diego Department of Pathology Stein Clinical Research Bldg. 9500 Gilman Drive La Jolla CA 92093-0679 Tel: 858 642 1106 -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: text/enriched Size: 1434 bytes Desc: not available URL: From sofia at substancia.com Wed Sep 22 11:27:07 2004 From: sofia at substancia.com (Ana Sofia Figueiredo) Date: Wed, 22 Sep 2004 15:27:07 -0000 Subject: [BiO BB] Bionformatics and System Biology Message-ID: <20040922141954.C267FD1F05@www.bioinformatics.org> Hi, As there is no consensus definition for Systems Biology nor for Bioinformatics, pointing out the differences and similarities amongst them is not straight forward. In my opinion, Systems Biology aims at understanding a biological system (for instace, a cell) as a whole. Instead of looking at the individual elements that constitute a cell, it studies how genes and proteins interact; how fluxes distribute in a metabolic pathway (and why); how does the system reacts to external perturbations, and tries to identify the mechanisms underlying the different phenomena. Then, this information will be used to construct mathematical models. The application of systems theory to biolgy is not new. Authors such as Bertalanffy, Robert Rosen, Savageau have described mathematically biological phenomena, based on engineering principles. Systems biology from those days differs from todays due to the huges amounts of information generated by disciplines as genomics, proteomics and metabolomics. This boom of information is generated by bioinformatics tools. Bioinformatics is the field of intersection between biology and computer sciences. It uses the power of computer sciences to store, analyse, integrate and visualise biological data, in order to answer biologists questions. These papers give a global perspective of systems biology: 1. Kitano H,Computational System Biology Nature (2002) 420; 206-210. 2. Kitano H, Systems Biology: A Brief Overview Science (2002) 295; 1662-1664. 3. Wolkenhauer O, Systems Biology: The reincarnation of systems theory applied to Biology? Briefings in Bioinformatics (2001) Vol. 2 No. 3 258-270. I hope this helps! Sofia --------- Mensagem Original -------- De: jareyes at utalca.cl Para: bio_bulletin_board at bioinformatics.org Assunto: [BiO BB] Bionformatics and System Biology Data: 22/09/04 10:59 > > > Hi, I am looking for information about the differences and similarities > between Bioinformatics and System Biology. > Do you know were can I found some papers, documents or other sources of > information about this? > > Thanks in advanced for yours comments. > > Jos? Antonio > > > ------------------------------------------------- > Este mensaje fue enviado por: http://utalca.cl > _______________________________________________ > 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 Fri Sep 24 09:25:38 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Fri, 24 Sep 2004 14:25:38 +0100 (BST) Subject: [BiO BB] What? Message-ID: Anyone else get the same thing as me typing this link in to a mozilla URL box... http://google/ This is either a local weirdness or totally strange. I get a webpage which is actually http://www.bio.org/ If I just type google into my mozilla url and hit return I get this page. Time was when this function returned the top google hit of the word entered (or was that firefox only?) http://localhost.be/ was a great use of that function. Is it just me? From szed4 at yahoo.com Fri Sep 24 13:58:16 2004 From: szed4 at yahoo.com (Shamshad Zarina) Date: Fri, 24 Sep 2004 10:58:16 -0700 (PDT) Subject: [BiO BB] What? In-Reply-To: Message-ID: <20040924175816.55728.qmail@web14003.mail.yahoo.com> Hi Dan, I get google main page when I used the link provided by you. I am using mozilla 1.5. regards, Shamshad --- Dan Bolser wrote: > > Anyone else get the same thing as me typing this > link in to a mozilla URL > box... > > http://google/ > > This is either a local weirdness or totally strange. > > I get a webpage which is actually > http://www.bio.org/ > > If I just type google into my mozilla url and hit > return I get this > page. Time was when this function returned the top > google hit of the word > entered (or was that firefox only?) > > http://localhost.be/ was a great use of that > function. > > Is it just me? > > > > _______________________________________________ > BiO_Bulletin_Board maillist - > BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From idoerg at burnham.org Mon Sep 27 12:11:19 2004 From: idoerg at burnham.org (Iddo) Date: Mon, 27 Sep 2004 09:11:19 -0700 Subject: [BiO BB] San Diegans :UniProt 2.0 Talks at UCSD - Tue, Wed, Thu this Week Message-ID: <41583BA7.2000506@burnham.org> For Bioinformaticists in the San Diego Area: ****** You are cordially invited to a series of talks at the San Diego Supercomputer Center Auditorium, September 28, 29, and 30th on UniProt 2.0 and Protein Kinase annotation to be presentd by Sandra Orchard and Samuel Kerrien (who will present instead of Ernst Kretschmann) from the EMBL - European Bioinformatics Institute. Specific details of each days talk is given below. Refreshments will be served. Questions or if you would like to meet with the guest speakers please contact Hannes Niedner (hannes at sdsc.edu) -------- Title:UniProt 2.0 - General Overview Date/Time/Place: September 28, 2004, SDSC Auditorium 1-2 pm seminar 2-3 pm technical discussion/walk through Speaker: Sandra Orchard EMBL - European Bioinformatics Institute Abstract: The Swiss-Prot, TrEMBL and PIR protein databaseactivities have united to form the Universal Protein Knowledgebase(UniProt) consortium, to provide a comprehensive,fully classified, richly and accurately annotated protein sequenceknowledgebase, with extensive cross-references and query interfaces.The central database will has two sections, corresponding tothe familiar Swiss-Prot (fully manually curated entries) andTrEMBL (enriched with automated classification, annotation andextensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases.The UniProt NREF (UniRef) databases provide representative subsetsof the knowledgebase suitable for efficient searching. The comprehensiveUniProt Archive (UniParc) is updated daily from many publicsource databases and includes many predicted and synthetic sequences which are not appropriate for inclusion within UniProt. ------- Title:UniProt 2.0 - Technical Overview & Discussion Date/Time/Place: September 29, 2004, SDSC Auditorium 3-4 pm Seminar 4-5 pm Technical Discussion Speaker: Samuel Kerrien EMBL - European Bioinformatics Institute Abstract: The annotation in gene and gene product is deeply rooted in a flat file/free text tradition. Relational or object oriented models of the data and their implementations are rare and usually have access restrictions for end users. Users of the UniProt data set, which is encompassing the former Swiss-Prot, TrEMBL and PIR content also has to deal with these legacy problems. The flat file format that has been used, extended and maintained over many years is readable for human eyes but difficult to process algorithmically. With the exponential growth of protein information, doubling the data amount approximately every two years, downloading the whole sets and parsing out what is actually needed on the end users side became cumbersome and CPU intensive. With UniProt, we are trying to overcome this situation and give users query access to our data sources. We are trying to make parsing procedures on the user side redundant by providing a solid interface to the data set as a whole and also to the individual protein entries. This presentation will give an overview over the libraries that are used at the EBI to present the UniProt data and to automatically process protein entries. Those libraries will be made available shortly for users and additional services are in the planning. The speaker will be going into some detail in terms of how to make use of the read only copy of the UniProt data base inside Java program code. ------ Title: UniProt 2.0 and the annotation of Protein Kinases Date/Time/Place: September 30, 2004, 1-2 pm, SDSC Auditorium Speaker: Sandra Orchard EMBL - European Bioinformatics Institute Abstract: A tour through the functionality of UniProt 2.0 will be provided with particular reference to annotation of members of the Protein Kinase family, one of the largest, and arguably best conserved protein families - members of which can be found in species as diverse as man and bacteria. The Swiss-Prot, TrEMBL and PIR protein databaseactivities have united to form the Universal Protein Knowledgebase(UniProt) consortium, to provide a comprehensive,fully classified, richly and accurately annotated protein sequenceknowledgebase, with extensive cross-references and query interfaces.The central database will has two sections, corresponding tothe familiar Swiss-Prot (fully manually curated entries) andTrEMBL (enriched with automated classification, annotation andextensive cross-references). For convenient sequence searches, UniProt also provides several non-redundant sequence databases.The UniProt NREF (UniRef) databases provide representative subsetsof the knowledgebase suitable for efficient searching. The comprehensiveUniProt Archive (UniParc) is updated daily from many publicsource databases and includes many predicted and synthetic sequences which are not appropriate for inclusion within UniProt. A tour through the functionality of UniProt 2.0 will be provided with particular reference to annotation of members of the Protein Kinase family, one of the largest, and arguably best conserved protein families - members of which can be found in species as diverse as man and bacteria. -- 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 Rajkumar.Bondugula at gmail.com Mon Sep 27 15:24:56 2004 From: Rajkumar.Bondugula at gmail.com (Raj) Date: Mon, 27 Sep 2004 14:24:56 -0500 Subject: [BiO BB] BLAST problems/Questions Message-ID: <33e68eb1040927122438b2e82f@mail.gmail.com> I am trying to search a local database with the profile of a sequence rather than a sequence itself. For this, I first generate profile for the sequence using 'nr' database and in the second step use the generated profile to search the local database. I use the 24/7/2004, windows version BLASTPGP program from NCBI website. I was running the following two commands in the same order: 1)'blastpgp -d nr -i seq.txt -j 3 -C profile.bin -o seq.out -a 2' 2)'blastpgp -d sel25culled -i seq.txt -R profile.bin -o seq0.txt -a 2' The first run is fine, but the second run produces the following lines: [NULL_Caption] WARNING: posReadCheckpoint: Attempting to recover data from previous checkpoint [NULL_Caption] WARNING: posReadCheckpoint: Data recovered successfully Why am I getting these messages, will these messages effect my results in anyway? Also, when I have ungapped alignments while search, I still see gaps inserted into the protein sequences in the output when I run the following command: 'blastpgp -d sel25culled -i seq.txt -R profile.bin -o seq0.txt -a 2 -g F' Why is this happening? is there anyway to have just ungapped alignment while searching? Regards, Raj =================================== Rajkumar Bondugula Digital Biology Laboratory 316 Engineering Bldg. North University of Missouri-Columbia =================================== From amackey at pcbi.upenn.edu Mon Sep 27 15:32:10 2004 From: amackey at pcbi.upenn.edu (Aaron J. Mackey) Date: Mon, 27 Sep 2004 15:32:10 -0400 Subject: [BiO BB] BLAST problems/Questions In-Reply-To: <33e68eb1040927122438b2e82f@mail.gmail.com> References: <33e68eb1040927122438b2e82f@mail.gmail.com> Message-ID: > Why am I getting these messages, will these messages effect my > results in anyway? These are "positive" notifications: everything worked fine. Checkpoint file usage is still considered "experimental" by NCBI, so these "debugging" statements are still there. Ignore them (unless it says "unsuccessful", of course). > Why is this happening? is there anyway to have just ungapped alignment > while searching? BLAST is a gap-capable algorithm; the fact that you've given it a profile instead of a "flat" scoring matrix doesn't change anything. If you'd like to prevent gaps, try raising the gap penalties ... -Aaron From bader at cbio.mskcc.org Mon Sep 27 21:18:25 2004 From: bader at cbio.mskcc.org (Gary Bader) Date: Mon, 27 Sep 2004 21:18:25 -0400 Subject: [BiO BB] Announcing Cytoscape Version 2.0 In-Reply-To: Message-ID: <003a01c4a4f9$0db31a70$8349a8c0@cbio.mskcc.org> Greetings, Cytoscape is an open-source bioinformatics software platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. http://www.cytoscape.org Version 2.0 Features: For users: -Load and save networks in SIF and GML formats -Load and visualize gene expression data -Visualize and lay out networks -Display network data in various ways using powerful visual styles -Network manager: easily organize multiple networks -Bird's eye view summary of network -Numerous plugins available for feature expansion and network analysis (more coming soon) E.g. Network filter, Gene expression data, Active Modules, MCODE See http://www.cytoscape.org/plugins2.php For programmers: -100% open-source -New open-source graph library (GINY) -New programmer API to ease plugin development Cytoscape is jointly developed by the groups of Benno Schwikowski (Pasteur Institute, Paris), Trey Ideker (University of California San Diego), Chris Sander (Memorial Sloan-Kettering Cancer Center) and Hamid Bolouri (Institute of Systems Biology, Seattle). Best regards, The Cytoscape Team Apologies if you receive this announcement more than once. We will try to avoid posting announcements to general mailing lists in the future. If you would like to stay informed of future Cytoscape developments, or if you would like to participate in the Cytoscape research community please visit http://cytoscape.org/community.php to sign up for one of our e-mail discussion or announcement lists. From suhaila_zainudin at fastmail.fm Mon Sep 27 22:36:17 2004 From: suhaila_zainudin at fastmail.fm (Suhaila Zainudin) Date: Mon, 27 Sep 2004 19:36:17 -0700 Subject: [BiO BB] Help with definitions Message-ID: <1096338977.19738.205283070@webmail.messagingengine.com> Hello, Can anyone provide the definition for the following terms? Thanks in advance. 1. gene-gene interaction/gene interaction 2. gene interaction network 3. gene network 4. gene regulatory network SZ -- Suhaila Zainudin suhaila_zainudin at fastmail.fm From Rajkumar.Bondugula at gmail.com Tue Sep 28 15:43:53 2004 From: Rajkumar.Bondugula at gmail.com (Raj) Date: Tue, 28 Sep 2004 14:43:53 -0500 Subject: [BiO BB] BLAST problems/Questions In-Reply-To: References: <33e68eb1040927122438b2e82f@mail.gmail.com> Message-ID: <33e68eb104092812436833ab4c@mail.gmail.com> Mackey, Thankyou very much for your answers. Regards, Raj On Mon, 27 Sep 2004 15:32:10 -0400, Aaron J. Mackey wrote: > > > Why am I getting these messages, will these messages effect my > > results in anyway? > > These are "positive" notifications: everything worked fine. Checkpoint > file usage is still considered "experimental" by NCBI, so these > "debugging" statements are still there. Ignore them (unless it says > "unsuccessful", of course). > > > Why is this happening? is there anyway to have just ungapped alignment > > while searching? > > BLAST is a gap-capable algorithm; the fact that you've given it a > profile instead of a "flat" scoring matrix doesn't change anything. If > you'd like to prevent gaps, try raising the gap penalties ... > > -Aaron > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From chrisg at bangor.ac.uk Fri Sep 24 09:54:26 2004 From: chrisg at bangor.ac.uk (Chris Gliddon) Date: Fri, 24 Sep 2004 14:54:26 +0100 Subject: [BiO BB] What? In-Reply-To: References: Message-ID: <41542712.6060402@bangor.ac.uk> As far as I can see, it's just you!! I get google when using both Firefox and Epiphany under Linux. Chris Dan Bolser wrote: >Anyone else get the same thing as me typing this link in to a mozilla URL >box... > >http://google/ > >This is either a local weirdness or totally strange. > >I get a webpage which is actually http://www.bio.org/ > >If I just type google into my mozilla url and hit return I get this >page. Time was when this function returned the top google hit of the word >entered (or was that firefox only?) > >http://localhost.be/ was a great use of that function. > >Is it just me? > > > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > -- ____________________________________________________ Dr. Chris Gliddon School of Biological Sciences University of Wales, Bangor LL57 2UW United Kingdom Tel: +44 (0)1248 382533 FAX: +44 (0)1248 382569 Mobile: +44 (0)7941 060423 ____________________________________________________ From dmb at mrc-dunn.cam.ac.uk Tue Sep 28 17:53:11 2004 From: dmb at mrc-dunn.cam.ac.uk (Dan Bolser) Date: Tue, 28 Sep 2004 22:53:11 +0100 (BST) Subject: [BiO BB] What? In-Reply-To: <41542712.6060402@bangor.ac.uk> Message-ID: Its crazy! Mozilla 1.4.2 Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.2) Gecko/20040308 type google in the URL, get a URL called http://google/ and a page from www.bio.org (which is also scary). It takes me here whatever word I type in the URL. On Fri, 24 Sep 2004, Chris Gliddon wrote: >As far as I can see, it's just you!! > >I get google when using both Firefox and Epiphany under Linux. > >Chris > >Dan Bolser wrote: > >>Anyone else get the same thing as me typing this link in to a mozilla URL >>box... >> >>http://google/ >> >>This is either a local weirdness or totally strange. >> >>I get a webpage which is actually http://www.bio.org/ >> >>If I just type google into my mozilla url and hit return I get this >>page. Time was when this function returned the top google hit of the word >>entered (or was that firefox only?) >> >>http://localhost.be/ was a great use of that function. >> >>Is it just me? >> >> >> >>_______________________________________________ >>BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board >> >> > > From sourangshu at csa.iisc.ernet.in Wed Sep 29 05:02:03 2004 From: sourangshu at csa.iisc.ernet.in (Sourangshu Bhattacharya) Date: Wed, 29 Sep 2004 14:32:03 +0530 Subject: [BiO BB] What? In-Reply-To: References: Message-ID: <415A7A0B.80101@csa.iisc.ernet.in> I think it tried to connect to http://google. In my case on Mozilla 1.6 Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.6) Gecko/20040113 It gave The requested URL could not be retrieved ------------------------------------------------------------------------ While trying to retrieve the URL: http://google.csa.iisc.ernet.in/ Please check with your local domain name administrator. Sourangshu Dan Bolser wrote: >Its crazy! > >Mozilla 1.4.2 >Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4.2) Gecko/20040308 > >type google in the URL, get a URL called http://google/ and a page from >www.bio.org (which is also scary). > >It takes me here whatever word I type in the URL. > >On Fri, 24 Sep 2004, Chris Gliddon wrote: > > > >>As far as I can see, it's just you!! >> >>I get google when using both Firefox and Epiphany under Linux. >> >>Chris >> >>Dan Bolser wrote: >> >> >> >>>Anyone else get the same thing as me typing this link in to a mozilla URL >>>box... >>> >>>http://google/ >>> >>>This is either a local weirdness or totally strange. >>> >>>I get a webpage which is actually http://www.bio.org/ >>> >>>If I just type google into my mozilla url and hit return I get this >>>page. Time was when this function returned the top google hit of the word >>>entered (or was that firefox only?) >>> >>>http://localhost.be/ was a great use of that function. >>> >>>Is it just me? >>> >>> >>> >>>_______________________________________________ >>>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 > > -- Sourangshu Bhattacharya PhD Student, Dept. of Computer Science & Automation, Indian Institute of Science, Bangalore - 560012, India. Website: http://people.csa.iisc.ernet.in/sourangshu Cell Phone : 91-98457 97492 From cysu at iis.sinica.edu.tw Thu Sep 30 04:00:32 2004 From: cysu at iis.sinica.edu.tw (Chia-Yu Su) Date: Thu, 30 Sep 2004 16:00:32 +0800 Subject: [Bio BB] Implementation or software packages of suffix tree Message-ID: <004701c4a6c3$92be8710$6300a8c0@emilysu> Hi, I want to construct suffix trees to extract repeats from sequences. I found several softwares from the web (by Dan Gusfield, Ting Chen, etc). Has anyone used any recommended suffix tree software? Are there any implementation or softwares of suffix trees which allows long sequence inputs and generate results in linear time? Please give me some suggestions about suffix tree software and where to download the web. Thanks a lot for your help! Best regards, Chia-Yu ------------ Chia-Yu Su Bioinformatics Program of Taiwan International Graduate Program Academia Sinica, Taiwan E-mail: cysu at iis.sinica.edu.tw Phone: +886-2-27883799 ext. 2302 Fax: +886-2-27824814 -------------- next part -------------- An HTML attachment was scrubbed... URL: