From Nadia.Bolshakova at cs.tcd.ie Tue May 6 06:24:08 2003 From: Nadia.Bolshakova at cs.tcd.ie (Nadia Bolshakova) Date: Tue, 6 May 2003 11:24:08 +0100 Subject: [BiO BB] Visualisation software Message-ID: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> Hi, I am looking for software which allows making chromosome maps and browse through them. Probably it could be some kind of interactive system for browsing through the maps and making and breaking connections. Thank you in advance for any recommendations, Nadia Bolshakova -------------- next part -------------- An HTML attachment was scrubbed... URL: From b.d.vanschaik at amc.uva.nl Tue May 6 07:00:36 2003 From: b.d.vanschaik at amc.uva.nl (Barbera van Schaik) Date: Tue, 06 May 2003 13:00:36 +0200 Subject: [BiO BB] Visualisation software References: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> Message-ID: <3EB795D4.3060905@amc.uva.nl> Hi Nadia, You can add own "tracks" (own information) at the UCSC genome browser: http://genome.ucsc.edu/cgi-bin/hgGateway?org=human (bottom of page) There are already links to other databases. If you want to make a browser yourself you can search for the existing code at bioperl.org and biojava.org Regards, Barbera Nadia Bolshakova wrote: > Hi, > > I am looking for software which allows making chromosome maps and > browse through them. Probably it could be some kind of interactive > system for browsing through the maps and making and breaking connections. > > Thank you in advance for any recommendations, > > Nadia Bolshakova > -- ._._._._._._._._._._._._._._._._._._._._._._. Barbera D.C. van Schaik Academic Medical Center (K2.207) Postbus 22660 1100 DD Amsterdam The Netherlands DivG/BioInformatics Laboratory DivC/Human Genetics Room: K2.207 Phone: (+31) 20 - 566 25 18 Email: B.D.vanSchaik at amc.uva.nl _._._._._._._._._._._._._._._._._._._._._._._ From hustlf at cs.cmu.edu Tue May 6 10:38:15 2003 From: hustlf at cs.cmu.edu (Li Fan) Date: Tue, 06 May 2003 10:38:15 -0400 Subject: [BiO BB] Visualisation software References: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> Message-ID: <3EB7C8D7.24DC91CC@cs.cmu.edu> Hello , I am doing some experiment on the AML/ALL microarray dataset. In the files, the author only provide the gene descriptions ,like id=1882 gene description: CST3 Cystatin C (amyloid angiopathy and cerebral hemorrhage) M27891\_at. id=6201 gene description: INTERLEUKIN-8 PRECURSOR Y00787\_s\_at id=4211 gene description: VIL2 Villin 2 (ezrin) X51521\_at. Could anyone tell me how to find search those genes from some standard database? (since the author does not provide the exact gene name) Thanks a lot Fan Li From p.pagel at gsf.de Tue May 6 10:56:39 2003 From: p.pagel at gsf.de (Philipp Pagel) Date: Tue, 6 May 2003 16:56:39 +0200 Subject: [BiO BB] Visualisation software In-Reply-To: <3EB7C8D7.24DC91CC@cs.cmu.edu> References: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> <3EB7C8D7.24DC91CC@cs.cmu.edu> Message-ID: <20030506145639.GA7912@porcupine.gsf.de> Hi! On Tue, May 06, 2003 at 10:38:15AM -0400, Li Fan wrote: > files, the author only provide the gene descriptions ,like > id=1882 [...] hemorrhage) M27891\_at. ^^^^^^ > id=6201 [...] INTERLEUKIN-8 PRECURSOR Y00787\_s\_at ^^^^^^ > id=4211 [...] VIL2 Villin 2 (ezrin) X51521\_at. ^^^^^^ The codes I marked with "^" appear to be Genbank accession numbers. So if you extract them from the file you can write a little script that gets the entries from the database. cu Philipp -- Dr. Philipp Pagel Tel. +49-89-3187-3675 Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 GSF - National Research Center for Environment and Health Ingolstaedter Landstrasse 1 85764 Neuherberg Germany From hustlf at cs.cmu.edu Tue May 6 16:00:55 2003 From: hustlf at cs.cmu.edu (Li Fan) Date: Tue, 06 May 2003 16:00:55 -0400 Subject: [BiO BB] Visualisation software References: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> <3EB7C8D7.24DC91CC@cs.cmu.edu> <20030506145639.GA7912@porcupine.gsf.de> Message-ID: <3EB81477.EFE5B90@cs.cmu.edu> Hello, Thank you very much for your help. My background is computer science and I have just started working in bioinformatics. I want to use bayesnetwork learning algorithm to learn two pathways which are related to AML/ALL disease from AML/ALL microarray data. (I say two pathways because we have found the data can be correctly classified by two groups of genes). Do you think it is feasible or if I have made some conceptual errors? Thank you. Fan Li Philipp Pagel wrote: > Hi! > > On Tue, May 06, 2003 at 10:38:15AM -0400, Li Fan wrote: > > files, the author only provide the gene descriptions ,like > > > id=1882 [...] hemorrhage) M27891\_at. > ^^^^^^ > > id=6201 [...] INTERLEUKIN-8 PRECURSOR Y00787\_s\_at > ^^^^^^ > > id=4211 [...] VIL2 Villin 2 (ezrin) X51521\_at. > ^^^^^^ > The codes I marked with "^" appear to be Genbank accession numbers. So > if you extract them from the file you can write a little script that > gets the entries from the database. > > cu > Philipp > > -- > Dr. Philipp Pagel Tel. +49-89-3187-3675 > Institute for Bioinformatics / MIPS Fax. +49-89-3187-3585 > GSF - National Research Center for Environment and Health > Ingolstaedter Landstrasse 1 > 85764 Neuherberg > Germany > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board From luciani at intelab.ufsc.br Tue May 6 10:26:42 2003 From: luciani at intelab.ufsc.br (Luciani Tatsch Piemolini) Date: Tue, 6 May 2003 11:26:42 -0300 Subject: [BiO BB] Protein structure Message-ID: <007401c313db$83c1fd40$2046a296@cpmd02> Hello, Can anyone suggest a program to construct a 3D structure of one protein sequence, that has demonstrated low homology with crystal structure in current databases? Sincerely Luciani Tatsch Piemolini -------------- next part -------------- An HTML attachment was scrubbed... URL: From hz5 at njit.edu Wed May 7 10:54:23 2003 From: hz5 at njit.edu (hz5 at njit.edu) Date: Wed, 07 May 2003 10:54:23 -0400 (EDT) Subject: [BiO BB] Visualisation software In-Reply-To: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> References: <015301c313b9$a0ffc4e0$6e26e286@DBNJK90J> Message-ID: <1052319263.3eb91e1fc35a5@webmail.njit.edu> ensemble(); http://www.ensembl.org/ Quoting Nadia Bolshakova : > Hi, > > I am looking for software which allows making chromosome maps and browse > through them. Probably it could be some kind of interactive system for > browsing through the maps and making and breaking connections. > > Thank you in advance for any recommendations, > > Nadia Bolshakova > > ========================================================= Haibo Zhang, PhD student Computational Biology, NJIT & Rutgers University Center for Applied Genomics, PHRI http://afs13.njit.edu/~hz5 From checkmevak at rediffmail.com Wed May 7 12:26:16 2003 From: checkmevak at rediffmail.com (V ARUN KUMAR) Date: 7 May 2003 16:26:16 -0000 Subject: [BiO BB] Accept subscribtion Message-ID: <20030507162616.25178.qmail@webmail7.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From idoerg at burnham.org Wed May 7 12:46:37 2003 From: idoerg at burnham.org (Iddo Friedberg) Date: Wed, 07 May 2003 09:46:37 -0700 Subject: [BiO BB] "Frontiers in Bioinformatics" -- room sharing? Message-ID: <3EB9386D.4000005@burnham.org> "Frontiers in Bioinformatics" symposium, June 6-8, 2003, Buffalo, NY Anybody going to that symposium, and wishes to share a room with a non-smoking male? ./I -- Iddo Friedberg, Ph.D. The Burnham Institute 10901 N. Torrey Pines Rd. La Jolla, CA 92037 USA Tel: +1 (858) 646 3100 x3516 Fax: +1 (858) 646 3171 http://bioinformatics.ljcrf.edu/~iddo From sandeep.dighe at siemens.com Wed May 7 10:16:17 2003 From: sandeep.dighe at siemens.com (Dighe Sandeep) Date: Wed, 7 May 2003 19:46:17 +0530 Subject: [BiO BB] Top ranked universities or centres for Bioinformatics Message-ID: <892CE977BB4FD31194EE00A0C9F273390B6F283E@blrk001a.sisl.co.in> Hello, Can anyone pls tell me about the top ranked universities or centres for Bioinformatics in the world, or direct me to some internet link where this information is available? Thank you, SD -------------- next part -------------- An HTML attachment was scrubbed... URL: From pajailwala at yahoo.com Wed May 7 15:25:11 2003 From: pajailwala at yahoo.com (Parthav Jailwala) Date: Wed, 7 May 2003 12:25:11 -0700 (PDT) Subject: [BiO BB] Top ranked universities or centres for Bioinformatics In-Reply-To: <892CE977BB4FD31194EE00A0C9F273390B6F283E@blrk001a.sisl.co.in> Message-ID: <20030507192511.49999.qmail@web12307.mail.yahoo.com> hi, try this link on the internet: http://bioinformatics.org/faq/#education hope it helps. Dighe Sandeep wrote: Hello, Can anyone pls tell me about the top ranked universities or centres for Bioinformatics in the world, or direct me to some internet link where this information is available? Thank you, SD ---------------------------------------------------------------------------------- Ask the experienced rather than the learned - An Arab Proverb --------------------------------------------------------------------------------- Parthav Jailwala,Analyst/Project Programmer,Max McGee National Centre for Juvenile Diabetes,Pediatrics(Endocrinology), Medical College of Wisconsin, Milwaukee, WI. Ph : 414-456-8269,E-mail : pajailwala at yahoo.com --------------------------------- Do you Yahoo!? The New Yahoo! Search - Faster. Easier. Bingo. -------------- next part -------------- An HTML attachment was scrubbed... URL: From purnatt at VALLEY.NET Wed May 7 16:50:01 2003 From: purnatt at VALLEY.NET (purnatt) Date: 07 May 2003 16:50:01 EDT Subject: [BiO BB] Protein structure Message-ID: <26460838@enfield.VALLEY.NET> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From gabriel.eichler at TCH.Harvard.edu Wed May 7 16:52:02 2003 From: gabriel.eichler at TCH.Harvard.edu (Gabriel Eichler) Date: Wed, 07 May 2003 16:52:02 -0400 Subject: [BiO BB] Bioinformatics Job Opening - Boston Message-ID: <000601c314da$83016a80$4626070a@R01897> The following is a job posting for the bioinformatics community. Please reply to gabriel.eichler at tch.harvard.edu with resumes of interested candidates. The Ingber Laboratory of the Vascular Biology Program, Children's Hospital of Boston and Harvard Medical School is seeking an entry-level bioinformatician to work on development of new software and analysis of high-dimensional gene microarray and proteomic data. Work place: The academic research laboratory of Dr. Donald Ingber combines computational approaches and novel software development strategies with "wet bench" experimental research. The laboratory includes scientists with various backgrounds, including physicists, engineers, and computer scientists, as well as molecular cell biologists and clinicians. Job Responsibilities: -Ports a prototype version of GEDI from Matlab into Java or C++. GEDI is a novel application software for analysis and expression of gene expression profile data that was recently developed by the Ingber laboratory. " Implements new features into the software, including new analysis algorithms and user interface modifications. -Analyzes gene expression profiling data obtained from ongoing research projects using this software and otheravailable software packages (SOM, hierarchical clustering). -Assists other scientists in basic computational tasks (data analysis and visualization) -Implements additional minor computational analysis tools, and assists in website development, as needed by the laboratory. Skills / Experience required -B.S./M.S. in computer science or experience in bioinformatics " Experience in application development in Java or C++, specifically: graphical programming and UI development; familiarity with Matlab a plus. " Knowledge of Microsoft Access and Excel (VBA). " Knowledge of undergraduate level biology / willing to expand knowledge into genomics and biomedical research. -Basic Knowledge of Web development (HTML, web graphics). Additional skills that would be a plus: -Familiarity with gene databases (GenBank, GeneOntology) -Familiarity with multivariate statistical analysis, and, specifically, technical issues related to gene expression profiling/proteomics " Knowledge of Matlab's Handle Graphics. Opportunities: -Interaction with a large variety of leading biomedical scientists working on several basic aspects of cancer, angiogenesis and tissue development. -Possibility to participate in research projects that may lead to authorship on publications or patents, and potential commercial applications. -Outstanding experience for future application to graduate or medical school Salary and Benefits: Annual salary TBD Start date: June 1, 2003 (flexible) -------------- next part -------------- An HTML attachment was scrubbed... URL: From isakti at hathway.com Fri May 9 07:29:26 2003 From: isakti at hathway.com (Suresh Swaminathan) Date: Fri, 09 May 2003 16:59:26 +0530 Subject: [BiO BB] Visualisation software References: <20030506160129.C842CD2919@www.bioinformatics.org> Message-ID: <019a01c3161e$3f938bd0$1601a8c0@isakti10> Hi, We have a Visualization software called Gene Picker, which is a proof of consept. Gene Picker is a web based tool that is developed to display Genetic Information in an easy to use graphical format. The objective is to enable the scientist to access Genetic information archived in a back end database through a graphical representation. This would enable the scientist to quickly seek and retrieve data useful to the research he is conducting. The basic search is done using a standard querying format of entering the text string into the search field and the relevant gene / intron is retrieved. The retrieved sequence is a text string of varying length and comprises the four nucleotides. Gene Picker is web based and is developed on open source platform. The main feature of Gene Picker is that it can be customized to a specific representation requirement of the Scientist. The application is scalable in that it can handle a huge volume of data and represent each retrieved sequence graphically and enable the end user to view all the annotations and enter annotations of their own. In a typical commercial deployment, more powerful search engines would be used to access data from multiple public and proprietary databases. If you would be interested , we could send you more details on Gene Picker and also give you a secured Login and password through you could browse through the application and get the feel of it. Looking forward to here from you, Warm Regards, Suresh Sakti Group, NY > > Message: 1 > From: "Nadia Bolshakova" > To: > Date: Tue, 6 May 2003 11:24:08 +0100 > Subject: [BiO BB] Visualisation software > Reply-To: bio_bulletin_board at bioinformatics.org > > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0150_01C313C2.02B11A10 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hi, > > I am looking for software which allows making chromosome maps and browse = > through them. Probably it could be some kind of interactive system for = > browsing through the maps and making and breaking connections.=20 > > Thank you in advance for any recommendations, > > Nadia Bolshakova > > From sa58794 at odin.mdacc.tmc.edu Fri May 9 17:06:39 2003 From: sa58794 at odin.mdacc.tmc.edu (clwu) Date: Fri, 09 May 2003 16:06:39 -0500 Subject: [BiO BB] Another visualization question In-Reply-To: <019a01c3161e$3f938bd0$1601a8c0@isakti10> References: <20030506160129.C842CD2919@www.bioinformatics.org> <019a01c3161e$3f938bd0$1601a8c0@isakti10> Message-ID: <3EBC185F.3030609@odin.mdacc.tmc.edu> Hi, Group, Is there anybody know how to generate a graph like the attachment to show a motif? I saw it often in publication. Thanks Cl From TFrederick at wyeth.com Sat May 10 12:00:53 2003 From: TFrederick at wyeth.com (Tom Frederick) Date: Sat, 10 May 2003 12:00:53 -0400 Subject: [BiO BB] Re:BiO_Bulletin_Board digest, Vol 1 #443 - 1 msg (Tom Frederick Out of the Office) Message-ID: I will be out of the office from 5/12 through 5/16/2003. For urgent SQL*LIMS connectivity issues, contact Ming Cui x1265 For urgent AffyLims or GEDS issues contact Chuck Borromeo x1898 Any other urgent matters, contact Debbie Mounts x1376. Thanks, Tom. From seabi at indiatimes.com Mon May 12 04:05:11 2003 From: seabi at indiatimes.com (seabi) Date: Mon, 12 May 2003 13:35:11 +0530 Subject: [BiO BB] Visualisation software Message-ID: <200305120739.NAA19594@WS0005.indiatimes.com> Mr. Suresh, for the benefit of our students studying PG courses in bioinformatics, I will be thankful if u could provide the link for he benefit of the students. malik bp e.mail:seabi at indiatimes.com bio_bulletin_board at bioinformatics.org wrote: Hi, We have a Visualization software called Gene Picker, which is a proof of consept. Gene Picker is a web based tool that is developed to display Genetic Information in an easy to use graphical format. The objective is to enable the scientist to access Genetic information archived in a back end database through a graphical representation. This would enable the scientist to quickly seek and retrieve data useful to the research he is conducting. The basic search is done using a standard querying format of entering the text string into the search field and the relevant gene / intron is retrieved. The retrieved sequence is a text string of varying length and comprises the four nucleotides. Gene Picker is web based and is developed on open source platform. The main feature of Gene Picker is that it can be customized to a specific representation requirement of the Scientist. The application is scalable in that it can handle a huge volume of data and represent each retrieved sequence graphically and enable the end user to view all the annotations and enter annotations of their own. In a typical commercial deployment, more powerful search engines would be used to access data from multiple public and proprietary databases. If you would be interested , we could send you more details on Gene Picker and also give you a secured Login and password through you could browse through the application and get the feel of it. Looking forward to here from you, Warm Regards, Suresh Sakti Group, NY > > Message: 1 > From: "Nadia Bolshakova" > To: > Date: Tue, 6 May 2003 11:24:08 +0100 > Subject: [BiO BB] Visualisation software > Reply-To: bio_bulletin_board at bioinformatics.org > > > This is a multi-part message in MIME format. > > ------=_NextPart_000_0150_01C313C2.02B11A10 > Content-Type: text/plain; > charset="iso-8859-1" > Content-Transfer-Encoding: quoted-printable > > Hi, > > I am looking for software which allows making chromosome maps and browse = > through them. Probably it could be some kind of interactive system for = > browsing through the maps and making and breaking connections.=20 > > Thank you in advance for any recommendations, > > Nadia Bolshakova > > _______________________________________________ BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org https://bioinformatics.org/mailman/listinfo/bio_bulletin_board Get Your Private, Free E-mail from Indiatimes at http://email.indiatimes.com Buy The Best In BOOKS at http://www.bestsellers.indiatimes.com Bid for Air Tickets @ Re.1 on Air Sahara Flights. Just log on to http://airsahara.indiatimes.com and Bid Now ! -------------- next part -------------- An HTML attachment was scrubbed... URL: From karen at scientecpersonnel.com Tue May 13 07:05:04 2003 From: karen at scientecpersonnel.com (Karen Tok) Date: Tue, 13 May 2003 19:05:04 +0800 Subject: [BiO BB] Jobs for PhDs Message-ID: Hi guys, We are a Executive Search company specialized in the recruitment for Life Science Ind in Asia. Currently we are looking for 2 PhDs in molecular and Cell Biology research guys for our client. Location : Singapore Company : US MNC (Stem Cell Research) Please email us your resume if you are keen to apply for this position. Thanks. 1) Position Title: Group Leader, Cell Biology Position Requirements: a.. A PhD graduate with at least 3 years experience, in mammalian cell biology, tissue culture, and some molecular biology background, or closely related disciplines, is required. The candidate must have a strong background in cell biology and tissue culture, with an interest in working with stem cells. b.. Experience in hematopoiesis and blood cells preferred. c.. Experience in mammalian cell processing, including experience with sterile laboratory technique required. d.. Experience and comfort in working with animal models and radioactive materials required. e.. Experience in flow cytometry and PCR preferred. f.. Familiarity with mammalian cell culture medium development preferred. g.. Working knowledge of statistical experimental design and analysis preferred. h.. The candidate will be encouraged to publish findings in research journals and focus on the application of research for commercial success Duties & Responsibilities: a.. Lead a small research group of research associates b.. The candidate will design, execute, and analyze experiments optimizing hematopoietic stem cell growth and purification process. Use cell biology, microscopy, histology, flow cytometry, tissue culture, and molecular biology techniques to understand and improve cell product. a.. The candidate will respond to needs from, and communicate results to, internal research teams of the company. b.. The candidate needs to be able to prepare seminar presentations and technical reports on findings 2) Position Title: Group Leader, Molecular Biology Position Requirements: a.. An PhD graduate with at least 3 years experience in molecular biology, with a special focus on mammalian cell systems. The candidate must have some background in cell biology and tissue culture, with an interest in working with stem cells. b.. Experience in group leadership and teamwork. c.. Experience with study of hematopoietic cells or blood cells preferred. d.. Experience in DNA chip and microarray analysis. e.. Working knowledge of statistical experimental design and analysis preferred. f.. The candidate will be encouraged to publish findings in research journals and focus on the application of research for commercial success. Duties & Responsibilities: a.. Lead a small research group of research associates b.. The candidate will design, execute, supervise and analyze experiments optimizing molecular techniques for gene expression analysis, gene isolation and functional expression cloning. The candidate will need to understand and use tissue culture, microscopy, histology, and flow cytometry techniques to understand and improve cell product. c.. The candidate will respond to needs from, and communicate results to, internal research teams of the company. d.. The candidate needs to be able to prepare seminar presentations and technical reports on findings Karen Tok Business Development Manager (Asia) Biomedical sciences, Healthcare, IT ScienTec Personnel No 5, Shenton Way, #37-02 UIC Building, Singapore 068808 Tel : 62253272 Fax : 62257282 HP : 91072139 karen at scientecpersonnel.com www.scientecpersonnel.com When one door closes, another opens. Seize the opportunity while the path remains lit. -------------- next part -------------- An HTML attachment was scrubbed... URL: From sa58794 at odin.mdacc.tmc.edu Thu May 15 12:19:06 2003 From: sa58794 at odin.mdacc.tmc.edu (clwu) Date: Thu, 15 May 2003 11:19:06 -0500 Subject: [BiO BB] Re: Another visualization question In-Reply-To: <005001c3178c$1bbb5cf0$1101a8c0@logic> References: <005001c3178c$1bbb5cf0$1101a8c0@logic> Message-ID: <3EC3BDFA.5030003@odin.mdacc.tmc.edu> Opps, somehow lost my attachment in my last email. Here it is. clwu Evgeny Cheremushkin wrote: > Hello clwu! > > I worked with visualisation of motifs, but there is no attachment in > your letter. Send me that picture, may be I'll be able to help you. > > cher. -------------- next part -------------- A non-text attachment was scrubbed... Name: untitled1.jpg Type: image/jpeg Size: 3230 bytes Desc: not available URL: From boris.steipe at utoronto.ca Thu May 15 13:07:19 2003 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Thu, 15 May 2003 13:07:19 -0400 Subject: [BiO BB] Re: Another visualization question References: <005001c3178c$1bbb5cf0$1101a8c0@logic> <3EC3BDFA.5030003@odin.mdacc.tmc.edu> Message-ID: <3EC3C946.B162D213@utoronto.ca> clwu wrote: > > Opps, somehow lost my attachment in my last email. Here it is. > Sequence Logos: introduced by Tom Schneider. Software availble. Very (!) useful. Best regards, Boris --- Boris Steipe University of Toronto Program in Proteomics & Bioinformatics Departments of Biochemistry & Molecular and Medical Genetics http://biochemistry.utoronto.ca/steipe From arunnuraa at rediffmail.com Thu May 15 14:51:27 2003 From: arunnuraa at rediffmail.com (Arun . A) Date: 15 May 2003 18:51:27 -0000 Subject: [BiO BB] Re: Another visualization question Message-ID: <20030515185127.17031.qmail@webmail17.rediffmail.com> Really it is very useful. Thank for Boris Steipe. For ur kind information. I am doing a project in peptide confirmation and coordinate generation if you are having anything regarding that it will useful for me. Thanking you On Thu, 15 May 2003 Boris Steipe wrote : >clwu wrote: > > > > Opps, somehow lost my attachment in my last email. Here it is. > > > > >Sequence Logos: introduced by Tom Schneider. Software availble. Very (!) useful. > > > > > >Best regards, > > >Boris > >--- >Boris Steipe >University of Toronto >Program in Proteomics & Bioinformatics >Departments of Biochemistry & Molecular and Medical Genetics >http://biochemistry.utoronto.ca/steipe >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board A.Arun, C/O Prof. M.R. N. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PERMANENT ADDRESS A.Arun, MSC Bioinformtics 34, Additional Hosteltel Bharathiar University Coimbatore-46 India Ph +91 422 2425092 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ___________________________________________________ Get email that means BUSINESS! me @ mycompany.com. Just Rs.1499/year. To start, click http://www.rediffmailpro.com From arunnuraa at rediffmail.com Sun May 18 10:44:00 2003 From: arunnuraa at rediffmail.com (Arun . A) Date: 18 May 2003 14:44:00 -0000 Subject: [BiO BB] discussion group Message-ID: <20030518144400.30318.qmail@webmail29.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From arunnuraa at rediffmail.com Sun May 18 11:00:57 2003 From: arunnuraa at rediffmail.com (Arun . A) Date: 18 May 2003 15:00:57 -0000 Subject: [BiO BB] Can u help Message-ID: <20030518150057.8233.qmail@webmail16.rediffmail.com> An embedded and charset-unspecified text was scrubbed... Name: not available URL: From basm101 at york.ac.uk Tue May 20 05:24:55 2003 From: basm101 at york.ac.uk (basm101) Date: Tue, 20 May 2003 10:24:55 +0100 Subject: [BiO BB] Bioperl FASTA to NEXUS with concatenation of genes Message-ID: <3EC9F467.12AE8C10@york.ac.uk> Hi there, I'm new to this board so not sure whether people use it to ask for help, if not I apologise for posting in the wrong place. I am wanting to concatenate gene datasets and wondered if anyone knew how to use bioperl to do this. My input files are aligned FASTA format and I would like the output to be NEXUS in non-interleaved format. ie. #NEXUS begin taxa; dimensions ntax=number of taxa; taxlabels labels here ; end; begin characters; dimensions nchar=number of chars; format symbols = "" missing=?; matrix [gene1] species 1 AAA species 2 BBB species 3 AAA [gene2] species1 CCC species2 DDD species3 CCC ; end; paup block here. I have a bioperl script that prints out in interleaved format, but I don't want this as I want to clearly see where one gene ends and the next begins. #!/usr/bin/perl -w #Bioperl for format conversions print "Which input file ?\n"; chomp($infile=); print "output filename:\n"; chomp($output=); open (MYFILE, "$infile" ) || die; open (DATA, ">$output" ) ||die; use Bio::AlignIO; $in = Bio::AlignIO->new(-file => "$infile" , '-format' => 'fasta'); $out = Bio::AlignIO->new(-file => ">$output" , '-format' => 'nexus'); # note: we quote -format to keep older perls from complaining. while ( my $aln = $in->next_aln() ) { $out->write_aln($aln); } @sequences = <$infile>; Also I need to make the AlignIO object take multiple input files. Any ideas ? Thanks, basm101 University of York From udprabhu1979 at hotmail.com Tue May 20 07:42:13 2003 From: udprabhu1979 at hotmail.com (prabhu balan) Date: Tue, 20 May 2003 17:12:13 +0530 Subject: [BiO BB] Can u help Message-ID: Hai Arun, Arun I am a post graduate in pharmacology (M.pharmacy). I am planning to do a post graduate diploma in bioinformatics. I am really confused regarding the quality institute offering bioinformatics. Suggest me in which institute i can try, I know i am disturbing you a lot. please reply me. Awaiting for your reply prabhu email prabhu_pcology at yahoo.com udprabhu1979 at hotmail.com >From: "Arun . A" >Reply-To: bio_bulletin_board at bioinformatics.org >To: absmith-gt at bioinformatics.org >Subject: [BiO BB] Can u help >Date: 18 May 2003 15:00:57 -0000 > >Respected Sir > Greetings. > I am working to develop a software for the cofirmation of protein >structure in C. I want to add a extra module for NeedleMan Wunch algorthim >or Smith Waterman algorithm to do sequence comparision. If any one having >the program with you help me by giving that one to me? > Thanking you. > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >A.Arun, >C/O Prof. M.R. N.Murthy, >Molecular BioPhysics, >Indian Institute of Science, >Bangalore. > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >PERMANENT ADDRESS >A.Arun, >MSC Bioinformtics >34, Additional Hosteltel >Bharathiar University >Coimbatore-46 >India >Ph +91 422 2425092 >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ >___________________________________________________ >Get email that means BUSINESS! me @ mycompany.com. >Just Rs.1499/year. >To start, click http://www.rediffmailpro.com > >_______________________________________________ >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board _________________________________________________________________ Bridge gaps. Reconnect with old friends. http://www.batchmates.com/msn.asp On batchmates.com From rong at bu.edu Tue May 20 11:28:38 2003 From: rong at bu.edu (Rong Chen) Date: Tue, 20 May 2003 11:28:38 -0400 (EDT) Subject: [BiO BB] Can u help In-Reply-To: Message-ID: Hi, prabhu The bioinformatics program in Boston University is one of fully developed bioinformatics programs in US. Check http://bioinfo.bu.edu/ for more details. rong ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Rong Chen Bioinformatics Program Boston University Boston, MA 02148 Tel: (617)358-1552(office) (617)283-8630(cell) Fax: (617)358-1067 E-mail: rong at bu.edu http://zlab.bu.edu/~rong ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ On Tue, 20 May 2003, prabhu balan wrote: > Hai Arun, > > Arun I am a post graduate in pharmacology (M.pharmacy). I am planning to do > a post graduate diploma in bioinformatics. I am really confused regarding > the quality institute offering bioinformatics. Suggest me in which institute > i can try, I know i am disturbing you a lot. please reply me. Awaiting for > your reply > prabhu > email > prabhu_pcology at yahoo.com > udprabhu1979 at hotmail.com > > >From: "Arun . A" > >Reply-To: bio_bulletin_board at bioinformatics.org > >To: absmith-gt at bioinformatics.org > >Subject: [BiO BB] Can u help > >Date: 18 May 2003 15:00:57 -0000 > > > >Respected Sir > > Greetings. > > I am working to develop a software for the cofirmation of protein > >structure in C. I want to add a extra module for NeedleMan Wunch algorthim > >or Smith Waterman algorithm to do sequence comparision. If any one having > >the program with you help me by giving that one to me? > > Thanking you. > > > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > >A.Arun, > >C/O Prof. M.R. N.Murthy, > >Molecular BioPhysics, > >Indian Institute of Science, > >Bangalore. > > > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >PERMANENT ADDRESS > >A.Arun, > >MSC Bioinformtics > >34, Additional Hosteltel > >Bharathiar University > >Coimbatore-46 > >India > >Ph +91 422 2425092 > >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > >___________________________________________________ > >Get email that means BUSINESS! me @ mycompany.com. > >Just Rs.1499/year. > >To start, click http://www.rediffmailpro.com > > > >_______________________________________________ > >BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > >https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > _________________________________________________________________ > Bridge gaps. Reconnect with old friends. http://www.batchmates.com/msn.asp > On batchmates.com > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From mtc0119 at isical.ac.in Wed May 21 03:06:01 2003 From: mtc0119 at isical.ac.in (Sourangshu Bhattacharya) Date: Wed, 21 May 2003 12:36:01 +0530 (IST) Subject: [BiO BB] Energy function for active site In-Reply-To: <20030518150057.8233.qmail@webmail16.rediffmail.com> Message-ID: Hi Everyone, I am a newbie to this group. I dont know whether this is the right plaace to ask such a question. Can anyone suggest me what are the avaiable energy functions for modelling the interactions between a ligand and the protein atoms. Thank you very much. Sourangshu Bhattacharya MTech Computer Science. From fhpk at hotmail.com Wed May 21 14:03:41 2003 From: fhpk at hotmail.com (Fabio Henrique Pfeilsticker de Knegt) Date: Wed, 21 May 2003 18:03:41 +0000 Subject: [BiO BB] Genome BOX Search Message-ID: Hi everyone, this is my debut message on this list. I?m glad that I?ve found you and I?m in need of some advice... I?m interested in searching for some special sequences, like TATA and PHO boxes, in a non-anotated bacterial genomic sequence (from TIGR UFMG) . What would be the best strategy for that? A blast search with the consensus sequence or something like a DNA motif search? Thank you, F?bio Henrique Pfeilsticker de Knegt, CBMEG - UNICAMP. Campinas-SP, Brasil. _________________________________________________________________ MSN Messenger: converse com os seus amigos online. http://messenger.msn.com.br From letondal at pasteur.fr Thu May 22 10:38:18 2003 From: letondal at pasteur.fr (Catherine Letondal) Date: Thu, 22 May 2003 16:38:18 +0200 Subject: [BiO BB] Genome BOX Search In-Reply-To: Your message of "Wed, 21 May 2003 18:03:41 -0000." Message-ID: <200305221438.h4MEcIhJ166835@electre.pasteur.fr> "Fabio Henrique Pfeilsticker de Knegt" wrote: > Hi everyone, this is my debut message on this list. I?m glad that I?ve > found you and I?m in need of some advice... > > I?m interested in searching for some special sequences, like TATA and PHO > boxes, in a non-anotated bacterial genomic sequence (from TIGR UFMG) . What > would be the best strategy for that? A blast search with the consensus > sequence or something like a DNA motif search? SMILE (Structured Motifs Inference and Evaluation) has been used for such type of searching (I believe) : http://www-igm.univ-mlv.fr/~marsan/smile_english.html > > Thank you, > > F?bio Henrique Pfeilsticker de Knegt, CBMEG - UNICAMP. Campinas-SP, > Brasil. > > _________________________________________________________________ > MSN Messenger: converse com os seus amigos online. > http://messenger.msn.com.br > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board -- Catherine Letondal -- Pasteur Institute Computing Center From Mauricio.Canales at biotec.utfsm.cl Thu May 22 07:03:25 2003 From: Mauricio.Canales at biotec.utfsm.cl (Mauricio Canales) Date: Thu, 22 May 2003 13:03:25 +0200 Subject: [BiO BB] Energy function for active site References: Message-ID: <005f01c32051$c477a100$e21801c8@mcanales> Hello Sourangshu Bhattacharya Depends on the caracteristics of the ligand. If it is a peptide a pretty known package is DOCK http://www.cmpharm.ucsf.edu/kuntz/. I used GRAMM, http://reco3.ams.sunysb.edu/gramm/ which was the best classified protein-protein docking procedure on CASP2 at the momment of the work. A model of amyloide peptide was docked onto acetylcholinesterase surface from Torpedo and it was experimentally tested. Energy functions are described in references at web pages. Normally they put more importance on nonbonded interactions: vanderwaals, electrostatics and h-bonds. I have not actualized later this topic so if you find other best procedures let me know it. Mauricio Center for Biotechnology UTFSM Valparaiso Chile Phone 56-32-654730 Fax 56-32- 654783 ----- Original Message ----- From: "Sourangshu Bhattacharya" To: Sent: Wednesday, May 21, 2003 9:06 AM Subject: [BiO BB] Energy function for active site > Hi Everyone, > I am a newbie to this group. I dont know whether this is the right plaace > to ask such a question. > > Can anyone suggest me what are the avaiable energy functions for modelling > the interactions between a ligand and the protein atoms. > > Thank you very much. > > Sourangshu Bhattacharya > MTech Computer Science. > > > _______________________________________________ > BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > From sebastien.vachenc at free.fr Fri May 23 04:09:12 2003 From: sebastien.vachenc at free.fr (Sebastien VACHENC) Date: Fri, 23 May 2003 10:09:12 +0200 (CEST) Subject: [BiO BB] ulpload file cgi perl Message-ID: <1053677352.3ecdd728d279c@imp.free.fr> Hi, I can't upload a .csv file to my server. In fact I try to load it in order to load it in a sql table by LOAD DATA INFILE 'XXX.csv' INTO ... How upload this type of file, and HOW use this file in my sql request ? Thanks, S?bastien From mtc0119 at isical.ac.in Sun May 25 10:00:28 2003 From: mtc0119 at isical.ac.in (Sourangshu Bhattacharya) Date: Sun, 25 May 2003 19:30:28 +0530 (IST) Subject: [BiO BB] Energy function for active site In-Reply-To: <005f01c32051$c477a100$e21801c8@mcanales> Message-ID: Dear Mr. Canales, Thank you very much for the information and very sorry for replying so late. Actually I wasn't looking for the packages but the explicit equations and constants that model the ligand-receptor interactions. Moreover, I believe DOCK is not freely available for download. Do you think, Hydrophobicity plays any role in such interactions ? Please let me know about your opinion. Thank you Sourangshu Bhattacharya ISI Kolkata. On Thu, 22 May 2003, Mauricio Canales wrote: > Hello Sourangshu Bhattacharya > > Depends on the caracteristics of the ligand. If it is a peptide a pretty > known package > is DOCK http://www.cmpharm.ucsf.edu/kuntz/. > I used GRAMM, http://reco3.ams.sunysb.edu/gramm/ > which was the best classified protein-protein docking procedure > on CASP2 at the momment of the work. A model of amyloide peptide was docked > onto acetylcholinesterase surface from Torpedo and it was experimentally > tested. > Energy functions are described in references at web pages. Normally > they put more importance on nonbonded interactions: vanderwaals, > electrostatics and h-bonds. > I have not actualized later this topic so if you find other best procedures > let me know it. > > Mauricio > > Center for Biotechnology > UTFSM > Valparaiso Chile > Phone 56-32-654730 > Fax 56-32- 654783 > > > ----- Original Message ----- > From: "Sourangshu Bhattacharya" > To: > Sent: Wednesday, May 21, 2003 9:06 AM > Subject: [BiO BB] Energy function for active site > > > > Hi Everyone, > > I am a newbie to this group. I dont know whether this is the right plaace > > to ask such a question. > > > > Can anyone suggest me what are the avaiable energy functions for modelling > > the interactions between a ligand and the protein atoms. > > > > Thank you very much. > > > > Sourangshu Bhattacharya > > MTech Computer Science. > > > > > > _______________________________________________ > > 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 M.Tech. Computer Science, Indian Statistical Institute, Kolkata. ---------------------------------------------------------------------------- From jgentry at jimmy.harvard.edu Fri May 30 02:00:03 2003 From: jgentry at jimmy.harvard.edu (Jeff Gentry) Date: Fri, 30 May 2003 02:00:03 -0400 (EDT) Subject: [BiO BB] Bioconductor 1.2 Released Message-ID: The Bioconductor development team announces release 1.2 of the Bioconductor packages for the analysis of genomic data. Bioconductor is an open source bioinformatics software project based on the R language. Version 1.2 features: ===================== * All packages from the 1.1 release are included. All current bug fixes have been applied, and most have been upgraded and provide enhanced functionality. * affy: The affy package now provides for the automatic downloads of necessary CDF packages. There is also a new function, justRMA() which will use less system resources if one just wants RMA vs. using ReadAffy() and then rma/expresso - this will solve some users' problem when they do not have enough memory for working with the full method. The package's implementation of MAS 5.0 now agrees better with Affymetrix's then in previous releases, and now includes a function mas5() to make it easier for a user to obtain these results. * affycomp: A new package that serves as a graphics toolbox for the assessment of Affymetrix expression measures. * AnnBuilder: DB support is no longer required. ABPkgBuilder now provides a signle API for building of data packages. Also, data packages built with AnnBuilder will include an evidence code and association information for GO ids. * Biobase: The exprs2excel method for the exprSet class has been added, which will create an excel friendly file from the expression component of an exprSet. * DynDoc: A new package that provides a set of functions to create and interact with dynamic documents and vignettes * limma: A new package that provides functionality to handle linear models for microarray data. * makecdfenv: A package to create hash table environments from CDF files, as well as functionality to create data packages out of these environments. * RBGL: A new package that provides an interface to the Boost libraries for graph manipulation. * Rgraphviz: A new package that provides an interface with Graphviz to plot graph objects in R. * Ruuid: A new package that provides Universally Unique ID values (UUIDs). * SAGElyzer: A new package that will store SAGE data in a database and then provide functionality to locate genes that are similar to a given SAGE tag. * tkWidgets: The importWizard functionality was added, which provides an Excel style interface for importing data into R. Also the DPExplorer is new in 1.2 - allowing users to explore a BioC data package. The argsWidget widget set will create a GUI for accepting input dynamically. * vsn: vsn can now be used as a normalization method with the affy package. The likelihood function optimization has been streamlined and is faster. There is a new function to produce a diagnostic plot for the variance-mean relationship of microarray data, meanSdPlot. The data returned by vsn is now an object of class "exprSet". * widgetTools: A new package that provides user friendly tools to create Tcl/Tk widgets in R. Software, documentation, and further details are available on the Bioconductor WWW site: http://www.bioconductor.org/ HELP AND RESOURCES: =================== Information on subscribing to the mailing list and viewing its archives can be found at: http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Please use that list to discuss Bioconductor specific issues, bugs, and problems. Note that every package has a vignette (a literate program which provides an annotated example of the package's use) as well as possibly some "HOWTO"s. These document the tool's usage, and are provided in the "doc" subdirectory of each package library. WHO: ==== For the Bioconductor development team: Douglas Bates, University of Wisconsin, USA. Vince Carey, Harvard Medical School, USA. Marcel Dettling, Federal Inst. Technology, Switzerland. Sandrine Dudoit, Division of Biostatistics, University of California, Berkeley, USA. Byron Ellis, Harvard Department of Statistics, USA. Laurent Gautier, Technial University of Denmark, Denmark. Robert Gentleman, Harvard Medical School, USA. Jeff Gentry, Dana-Farber Cancer Institute, USA. Kurt Hornik, Technische Universitat Wien, Austria. Torsten Hothorn, Institut fuer Medizininformatik, Biometrie und Epidemiologie, Germany. Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis, Germany. Stefano Iacus, Italy Rafael Irizarry, Department of Biostatistics (JHU), USA. Friedrich Leisch, Technische Universitat Wien, Austria. Martin Maechler, Federal Inst. Technology, Switzerland. Anthony Rossini, University of Washington and the Fred Hutchinson Cancer Research Center, USA. Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany. Gordon Smythe, WEHI Bioinformatics Group, Australia Luke Tierney, University of Iowa, USA. Jean Yee Hwa Yang, University of California, San Francisco, USA. Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA