From gary at bioinformatics.org Mon Feb 5 13:02:55 2001 From: gary at bioinformatics.org (Gary Van Domselaar) Date: Mon, 5 Feb 2001 13:02:55 -0500 (EST) Subject: [BiO BB] Test Message-ID: Testing the bio BB mailing list. From paolo at ibm43p.biotech.ist.unige.it Tue Feb 13 03:22:14 2001 From: paolo at ibm43p.biotech.ist.unige.it (Paolo Romano) Date: Tue, 13 Feb 2001 09:22:14 +0100 (NFT) Subject: [BiO BB] Call for Papers: NETTAB Workshop Message-ID: <200102130822.JAA15398@ibm43p.biotech.ist.unige.it> Dear members, a call for contribution is now open for the NETTAB Workshop on: CORBA and XML: Towards a bioinformatics integrated network environment May 17th-18th, 2001 Advanced Biotechnology Center, Genova, Italy http://www.cba.unige.it/Events/NETTAB/ This workshop will try to introduce the evolving standardization activities for bioinformatics, mainly represented by CORBA and XML based efforts, and outline, through the final round table, the most probable scenarios of coming years. TOPICS * Emerging network standards and their application in the integration of distributed environments. Related facilities and services. Role of ontologies in biology standardization. * New standards, servers, clients and applications in the field of molecular biology and biotechnology, with emphasis on bioinformatics. * Use of programming languages for the exploitation of the integration of distributed databases and software: Perl, Java, Python, PHP, other "open source" languages. Libraries for bioinformatics applications. * Integrated systems and software, SRS implementations. The following lectures have already been defined. * Interoperability of data banks and software systems in the (post) Internet era, Luca Toldo, Merck KGaA, Germany * Standardization and ontologies in biology, Steffen Schulze-Kremer, RZPD, Germany * MGED and MAML: a joint effort for Microarray and Gene Expression standardization, Alvis Brazma, European Bioinformatics Institute, United Kingdom * Current CORBA development activities at the European Bioinformatics Institute, Philip Ljinzaad, European Bioinformatics Institute, United Kingdom * Current efforts and perspectives in the use of XML for biology and the XEWA initiative, Terence Critchlow, Lawrence Livermore National Laboratory, USA * The BioCorba specification and its implementation in java, perl and python, Matthew Pocock, The Sanger Centre, United Kingdom * Integration of SRS with the Object Management Architecture and biology oriented extensible markup languages, Thure Etzold, Lion Biosciences Ltd, United Kingdom * AppLab and the development of network applications in biology, Martin Senger, European Bioinformatics Institute, United Kingdom * The TAMBIS project and its integration in the bioinformatics network environment, Carole Goble, University of Manchester, United Kingdom * The electronical infrastructure for the analysis of metabolic networks, Ralf Hofestaedt, University of Magdeburg, Germany * XML, XSLT and XMAS - application and limitations of XML in handling protein structure data, Andrew C.R. Martin, University of Reading, United Kingdom All workshop's topics are addressed. For submitting a contribution, an extended abstract (max 2 A4 pages, PDF format) will have to be submitted via a Submission Form at: http://www.cba.unige.it/Events/NETTAB/rform.html The deadline is March 1st, 2001. Notifications of acceptance will be sent within April 1st, 2001. Accepted communications and posters will have to submit a short paper (3 to 5 A4 pages) for the Conference Proceedings within May 1st, 2001. The following contributions are sought: * Communications and posters A limited number of oral communications will be selected and admitted to the Oral Communications Session on Friday 18th. The poster session will be in the afternoon of the 17th . * Demo of clients/servers applications A demo session will be held on the 18th. A computer room will be available for demonstrating bioinformatics related network applications based on CORBA and XML clients and servers. Researchers wishing to demonstrate their softwares are invited to submit a poster as well. * Communications (companies' session) A session will be devoted to the presentation of softwares developed by companies. Interested companies should get in touch with the Workshop Secretariat. NETTAB Workshop, Servizio Biotecnologie, Istituto Nazionale per la Ricerca sul Cancro, c/o Centro Biotecnologie Avanzate, Largo Rosanna Benzi 10, I-16132 Genova, Italy Fax: +39-010-5737295 Email: nettab at ist.unige.it Web site: http://www.cba.unige.it/Events/NETTAB/ REGISTRATION FEE Before May 1st, 2001: Academic: 150 Euro Non-academic: 300 Euro After May 1st, 2001: Academic: 200 Euro Non-academic: 400 Euro Fees include coffee breaks, lunches, social dinner, abstracts' book. Looking forward to seeing you in Genoa. Best regards. Paolo Romano (Workshop Chairman) -- Paolo Romano (paolo at ist.unige.it) Biotechnology Department, Natl Inst. for Cancer Research c/o Advanced Biotechnology Centre Largo Rosanna Benzi, 10, I-16132, Genova, Italy Tel: +39-010-5737-288 - Fax: +39-010-5737-295 From yyodogawa at asia-net.com Tue Feb 13 20:47:57 2001 From: yyodogawa at asia-net.com (Yugo Yodogawa) Date: Wed, 14 Feb 2001 10:47:57 +0900 Subject: [BiO BB] Job Opportunity (Bioinformatics/Molecular Modeling) - Tokyo, Japan Message-ID: Dear BIO Bulletin Board members, Apologies to those for whom this is of no interest. I am currently helping a friend/client in Tokyo find an English-speaking researcher for the position of Application Scientist at his company. Any experience in bioinformatics or molecular modeling would be gratefully appreciated, and overseas candidates are encouraged to apply. For more information on this position, please visit the following link: http://www.asia-net.com/show_job.php3?id=10716 Thank you very much for your time. Yugo Yodogawa Asia-Net K.K. From marielle at virtutech.se Wed Feb 14 04:28:24 2001 From: marielle at virtutech.se (Marielle Fois) Date: Wed, 14 Feb 2001 10:28:24 +0100 (CET) Subject: [BiO BB] Introducing into Bioinformatics Message-ID: <14986.20408.903595.245833@tuttle.hq.vtech> Hello, Does anybody have an idea of a good way of getting into bioinformatics for someone on computer science with no biology background? I wonder if there is a book or article considered the standard in bioinformatics. Wouldn't this be a good information to have in this site? Thanks, Marielle From gvd at penguin.pharmacy.ualberta.ca Wed Feb 14 09:29:53 2001 From: gvd at penguin.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Wed, 14 Feb 2001 07:29:53 -0700 (MST) Subject: [BiO BB] Introducing into Bioinformatics In-Reply-To: <14986.20408.903595.245833@tuttle.hq.vtech> Message-ID: Marielle, One of the best-selling books on bioinformatics is "Bioinformatics - A Practical Guide to the Analysis of Genes and Proteins," Baxevanis and Oulette (Wiley, 1998)". I found it to be very accessible. Another early, but still valuable book is "Sequence Analysis Primer" by Gribskov (1991). A less accessible, but still valuable book IMO, is "Bioinformatics, The Machine Learning Approach" by Baldi and Brunak. If you have no biology background, you might want to pick up a good molecular biology text. "Molecular Biology of the Cell" by James Watson (of Watson/Crick fame) is very good. Regards, g. -- -- Gary Van Domselaar Ph.D. Candidate, Associate Director, Faculty of Pharmacy, Bioinformatics.org: The Open Lab University of Alberta gary at bioinformatics.org gary at penguin.pharmacy.ualberta.ca http://bioinformatics.org/gary -- -- On Wed, 14 Feb 2001, Marielle Fois wrote: > Hello, > > Does anybody have an idea of a good way of getting into bioinformatics > for someone on computer science with no biology background? I wonder > if there is a book or article considered the standard in > bioinformatics. Wouldn't this be a good information to have in this > site? > > Thanks, > Marielle > > _______________________________________________ > BIO_Bulletin_Board maillist - BIO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > From Deanne.Taylor at pfizer.com Wed Feb 14 09:55:20 2001 From: Deanne.Taylor at pfizer.com (Taylor, Deanne) Date: Wed, 14 Feb 2001 09:55:20 -0500 Subject: [BiO BB] Introducing into Bioinformatics Message-ID: <35AAFCDE1F5FD4118B7F00508B60945C03164284@aadino.research.aa.wl.com> Besides the books that Gary listed, there really aren't any "Here's how to become a cutting-edge bioinformaticist" books out there. Bioinformatics is so new that most books that come out are all about the tools that exist, not how to build new or better tools. As a programmer, I doubt you'll want to sit back and use other people's tools. :) but those are just the books! There is so much for a programmer to do in bioinformatics that books just can't touch. Ah, but one or two more books. :) If you're of a mathematical bent, you may want to at least check out of the library Eddy's book "Biological Sequence Analysis" by Durbin, Eddy, Krogh and Mitchison. There are several new bioinformatics books out there that have just come out (search "bioinformatics" on Amazon.com), though from what I've seen they're on the level of Baxevanis, which is pretty much user-level stuff....how to use other people's software. Now, as a programmer, bioinformatics can become pretty much just about handling data sets. If you want to do the science of bioinformatics, you should follow what Gary said, definitely, and read up on the Mol. Bio of the Cell. Also is the book GENES VII by Ben Lewin for genomic info. If you want to work with genome or sequence information, you should know about stuff like open reading frames, restriction sites, and how the data is generated (PCR, etc). In addition to sequence manipulation, there are several avenues a programmer can explore. One is pure database handling, which reduces the bioinformatics problem down to a data structure level. For instance, expression profiles from chip data can be pretty big databases at big companies. Oracle is used a lot in many companies for this purpose. Additionally, data analysis and statistics are valuable, though many chip manufacturers supply the analysis programs so there isn't a need to do any more than understand what's going on when one is doing this kind of analysis. The bioinformatics field is really wide open as far as what one can do with the data sets. Manipulating large data sets is going to become very important in industry soon, including database work, because the real information isn't in the "genome"...it's in how the cells express it, and to do true expression profiling work takes thousands of experiments with many many data points. Also coming up in importance in industry is pharmo-chemical profiling...mix expression profiling with chemical profiles. Again, all database work but statistics become important since there are no commercial/validated programs for pharmochemical profiling so someone has to both set up the database schema as well as work on the validation of data sets. Summary: iif you want to be on the cutting-edge of bioinformatics, have a basic knowledge of statistics and validation, Perl and/or Python, Oracle/SQL, molecular biology and genetics. You can be a bioinformaticist without knowing much about mol bio and genetics, but you'll be more like a data handler (which most bioinf programmers are these days). Deanne Taylor -----Original Message----- From: Gary Van Domselaar [mailto:gvd at penguin.pharmacy.ualberta.ca] Sent: Wednesday, February 14, 2001 9:30 AM To: im99_foa at nada.kth.se Cc: BIO Bulletin Board Subject: Re: [BiO BB] Introducing into Bioinformatics Marielle, One of the best-selling books on bioinformatics is "Bioinformatics - A Practical Guide to the Analysis of Genes and Proteins," Baxevanis and Oulette (Wiley, 1998)". I found it to be very accessible. Another early, but still valuable book is "Sequence Analysis Primer" by Gribskov (1991). A less accessible, but still valuable book IMO, is "Bioinformatics, The Machine Learning Approach" by Baldi and Brunak. If you have no biology background, you might want to pick up a good molecular biology text. "Molecular Biology of the Cell" by James Watson (of Watson/Crick fame) is very good. Regards, g. -- -- Gary Van Domselaar Ph.D. Candidate, Associate Director, Faculty of Pharmacy, Bioinformatics.org: The Open Lab University of Alberta gary at bioinformatics.org gary at penguin.pharmacy.ualberta.ca http://bioinformatics.org/gary -- -- On Wed, 14 Feb 2001, Marielle Fois wrote: > Hello, > > Does anybody have an idea of a good way of getting into bioinformatics > for someone on computer science with no biology background? I wonder > if there is a book or article considered the standard in > bioinformatics. Wouldn't this be a good information to have in this > site? > > Thanks, > Marielle > > _______________________________________________ > BIO_Bulletin_Board maillist - BIO_Bulletin_Board at bioinformatics.org > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > _______________________________________________ BIO_Bulletin_Board maillist - BIO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board From miller at pharm.sunysb.edu Wed Feb 14 11:13:03 2001 From: miller at pharm.sunysb.edu (miller) Date: Wed, 14 Feb 2001 11:13:03 -0500 Subject: [BiO BB] Bioinformatics reading list (Was Introducing into Bioinformatics) References: <35AAFCDE1F5FD4118B7F00508B60945C03164284@aadino.research.aa.wl.com> Message-ID: <3A8AAE8F.D93FEAC5@pharm.sunysb.edu> Hi Everyone! I think that Marielle has a great idea here. We could start with the books and information provided by Gary and Deanne and expand from there. I would be willing to work on this if you like. Let me take this opportunity to introduce myself. I am a biochemist. I am not a programmer (yet) but I really love working with computers and would like to move further in that direction. I feel that bioinformatics is really an exciting area and I would like to work in this field. In addition, I am a strong supporter of open source software and free access to information. Holly -- ____________________________________________________________________________ Holly Miller, Ph.D. voice: 631 444-8018 Res. Asst. Prof. FAX: 631 444-7641 Dept. Pharm. Sci. http://www.pharm.sunysb.edu/faculty/miller/ SUNY Stony Brook miller at pharm.sunysb.edu Stony Brook, NY 11794-8651 **************************************************************************** BioMail--New references from Medline to your e-mail account http://biomail.sourceforge.net/biomail http://www.biomail.org ___________________________________________________________________________ "Taylor, Deanne" wrote: > Besides the books that Gary listed, there really aren't any "Here's how to > become a cutting-edge bioinformaticist" books out there. Bioinformatics is > so new that most books that come out are all about the tools that exist, not > how to build new or better tools. As a programmer, I doubt you'll want to > sit back and use other people's tools. :) but those are just the books! > There is so much for a programmer to do in bioinformatics that books just > can't touch. > > Ah, but one or two more books. :) If you're of a mathematical bent, you may > want to at least check out of the library Eddy's book "Biological Sequence > Analysis" by Durbin, Eddy, Krogh and Mitchison. There are several new > bioinformatics books out there that have just come out (search > "bioinformatics" on Amazon.com), though from what I've seen they're on the > level of Baxevanis, which is pretty much user-level stuff....how to use > other people's software. > > Now, as a programmer, bioinformatics can become pretty much just about > handling data sets. If you want to do the science of bioinformatics, you > should follow what Gary said, definitely, and read up on the Mol. Bio of the > Cell. Also is the book GENES VII by Ben Lewin for genomic info. If you want > to work with genome or sequence information, you should know about stuff > like open reading frames, restriction sites, and how the data is generated > (PCR, etc). > > In addition to sequence manipulation, there are several avenues a programmer > can explore. One is pure database handling, which reduces the bioinformatics > problem down to a data structure level. For instance, expression profiles > from chip data can be pretty big databases at big companies. Oracle is used > a lot in many companies for this purpose. Additionally, data analysis and > statistics are valuable, though many chip manufacturers supply the analysis > programs so there isn't a need to do any more than understand what's going > on when one is doing this kind of analysis. > > The bioinformatics field is really wide open as far as what one can do with > the data sets. Manipulating large data sets is going to become very > important in industry soon, including database work, because the real > information isn't in the "genome"...it's in how the cells express it, and to > do true expression profiling work takes thousands of experiments with many > many data points. > > Also coming up in importance in industry is pharmo-chemical profiling...mix > expression profiling with chemical profiles. Again, all database work but > statistics become important since there are no commercial/validated programs > for pharmochemical profiling so someone has to both set up the database > schema as well as work on the validation of data sets. > > Summary: iif you want to be on the cutting-edge of bioinformatics, have a > basic knowledge of statistics and validation, Perl and/or Python, > Oracle/SQL, molecular biology and genetics. You can be a bioinformaticist > without knowing much about mol bio and genetics, but you'll be more like a > data handler (which most bioinf programmers are these days). > > Deanne Taylor > > -----Original Message----- > From: Gary Van Domselaar [mailto:gvd at penguin.pharmacy.ualberta.ca] > Sent: Wednesday, February 14, 2001 9:30 AM > To: im99_foa at nada.kth.se > Cc: BIO Bulletin Board > Subject: Re: [BiO BB] Introducing into Bioinformatics > > Marielle, > > One of the best-selling books on bioinformatics is "Bioinformatics - A > Practical Guide to the Analysis of Genes and Proteins," Baxevanis and > Oulette (Wiley, 1998)". I found it to be very accessible. Another early, > but still valuable book is "Sequence Analysis Primer" by Gribskov (1991). > A less accessible, but still valuable book IMO, is "Bioinformatics, The > Machine Learning Approach" by Baldi and Brunak. If you have no biology > background, you might want to pick up a good molecular biology text. > "Molecular Biology of the Cell" by James Watson (of Watson/Crick fame) is > very good. > > Regards, > > g. > -- -- > Gary Van Domselaar > Ph.D. Candidate, Associate Director, > Faculty of Pharmacy, Bioinformatics.org: The Open Lab > University of Alberta gary at bioinformatics.org > gary at penguin.pharmacy.ualberta.ca http://bioinformatics.org/gary > -- -- > > On Wed, 14 Feb 2001, Marielle Fois wrote: > > > Hello, > > > > Does anybody have an idea of a good way of getting into bioinformatics > > for someone on computer science with no biology background? I wonder > > if there is a book or article considered the standard in > > bioinformatics. Wouldn't this be a good information to have in this > > site? > > > > Thanks, > > Marielle From gvd at penguin.pharmacy.ualberta.ca Wed Feb 14 13:46:31 2001 From: gvd at penguin.pharmacy.ualberta.ca (Gary Van Domselaar) Date: Wed, 14 Feb 2001 11:46:31 -0700 (MST) Subject: [BiO BB] Bioinformatics reading list (Was Introducing into Bioinformatics) In-Reply-To: <3A8AAE8F.D93FEAC5@pharm.sunysb.edu> Message-ID: On Wed, 14 Feb 2001, miller wrote: > Hi Everyone! > > I think that Marielle has a great idea here. We could start with the books and > information provided by Gary and Deanne and expand from there. I would be > willing to work on this if you like. That is a good idea. If you want to write up the web pages for it, I'll definitely post them on the site. If you need an account, let me know and I'll set it up for you. g. -- From bioinformaticsckk at yahoo.co.in Wed Feb 14 23:32:04 2001 From: bioinformaticsckk at yahoo.co.in (=?iso-8859-1?q?kiran=20challapalli?=) Date: Thu, 15 Feb 2001 04:32:04 +0000 (GMT) Subject: [BiO BB] Re: BIO_Bulletin_Board digest, Vol 1 #3 - 5 msgs In-Reply-To: <200102141700.MAA13413@www.bioinformatics.org> Message-ID: <20010215043204.2182.qmail@web8001.mail.in.yahoo.com> Hello everyone, Let me introduce myself. I am Kiran kumar working as a Bioinformatics scientist. I like this kind of interaction and i appreciate the people who are participating in this activity. It's nice that Marielle got quite a bit of information related to bioinformatics books. I also request you all to find some time to join in my bioinformatics club and share our knowledge. The webadress is- http://in.clubs.yahoo.com/clubs/kiransbioinformaticsfriends With best wishes, Kiran Kumar.c --- bio_bulletin_board-admin at bioinformatics.org wrote: > > Send BIO_Bulletin_Board maillist submissions to > bio_bulletin_board at bioinformatics.org > > To subscribe or unsubscribe via the web, visit > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > or, via email, send a message with subject or body > 'help' to > bio_bulletin_board-request at bioinformatics.org > You can reach the person managing the list at > bio_bulletin_board-admin at bioinformatics.org > > When replying, please edit your Subject line so it > is more specific than > "Re: Contents of BIO_Bulletin_Board digest...") > > > Today's Topics: > > 1. Job Opportunity (Bioinformatics/Molecular > Modeling) - Tokyo, Japan (Yugo Yodogawa) > 2. Introducing into Bioinformatics (Marielle Fois) > 3. Re: Introducing into Bioinformatics (Gary Van > Domselaar) > 4. RE: Introducing into Bioinformatics (Taylor, > Deanne) > 5. Bioinformatics reading list (Was Introducing > into Bioinformatics) (miller) > > --__--__-- > > Message: 1 > Reply-To: > From: "Yugo Yodogawa" > To: > Subject: [BiO BB] Job Opportunity > (Bioinformatics/Molecular Modeling) - Tokyo, Japan > Date: Wed, 14 Feb 2001 10:47:57 +0900 > charset="iso-2022-jp" > > Dear BIO Bulletin Board members, > > Apologies to those for whom this is of no interest. > > I am currently helping a friend/client in Tokyo find > an English-speaking > researcher for the position of Application Scientist > at his company. > Any experience in bioinformatics or molecular > modeling would be > gratefully appreciated, and overseas candidates are > encouraged to > apply. > > For more information on this position, please visit > the following link: > http://www.asia-net.com/show_job.php3?id=10716 > > Thank you very much for your time. > > Yugo Yodogawa > Asia-Net K.K. > > --__--__-- > > Message: 2 > From: Marielle Fois > Date: Wed, 14 Feb 2001 10:28:24 +0100 (CET) > To: BIO Bulletin Board > > Subject: [BiO BB] Introducing into Bioinformatics > Reply-To: im99_foa at nada.kth.se > > Hello, > > Does anybody have an idea of a good way of getting > into bioinformatics > for someone on computer science with no biology > background? I wonder > if there is a book or article considered the > standard in > bioinformatics. Wouldn't this be a good information > to have in this > site? > > Thanks, > Marielle > > --__--__-- > > Message: 3 > Date: Wed, 14 Feb 2001 07:29:53 -0700 (MST) > From: Gary Van Domselaar > > To: > cc: BIO Bulletin Board > > Subject: Re: [BiO BB] Introducing into Bioinformatics > > Marielle, > > One of the best-selling books on bioinformatics is > "Bioinformatics - A > Practical Guide to the Analysis of Genes and > Proteins," Baxevanis and > Oulette (Wiley, 1998)". I found it to be very > accessible. Another early, > but still valuable book is "Sequence Analysis > Primer" by Gribskov (1991). > A less accessible, but still valuable book IMO, is > "Bioinformatics, The > Machine Learning Approach" by Baldi and Brunak. If > you have no biology > background, you might want to pick up a good > molecular biology text. > "Molecular Biology of the Cell" by James Watson (of > Watson/Crick fame) is > very good. > > Regards, > > g. > -- > -- > Gary Van Domselaar > Ph.D. Candidate, > Associate Director, > Faculty of Pharmacy, > Bioinformatics.org: The Open Lab > University of Alberta > gary at bioinformatics.org > gary at penguin.pharmacy.ualberta.ca > http://bioinformatics.org/gary > -- > -- > > > > On Wed, 14 Feb 2001, Marielle Fois wrote: > > > Hello, > > > > Does anybody have an idea of a good way of getting > into bioinformatics > > for someone on computer science with no biology > background? I wonder > > if there is a book or article considered the > standard in > > bioinformatics. Wouldn't this be a good > information to have in this > > site? > > > > Thanks, > > Marielle > > > > _______________________________________________ > > BIO_Bulletin_Board maillist - > BIO_Bulletin_Board at bioinformatics.org > > > http://bioinformatics.org/mailman/listinfo/bio_bulletin_board > > > > > --__--__-- > > Message: 4 > From: "Taylor, Deanne" > To: im99_foa at nada.kth.se, > "'gvd at penguin.pharmacy.ualberta.ca'" > > Cc: BIO Bulletin Board > > Subject: RE: [BiO BB] Introducing into Bioinformatics > Date: Wed, 14 Feb 2001 09:55:20 -0500 > charset="iso-8859-1" > > Besides the books that Gary listed, there really > aren't any "Here's how to > become a cutting-edge bioinformaticist" books out > there. Bioinformatics is > so new that most books that come out are all about > the tools that exist, not > how to build new or better tools. As a programmer, I > doubt you'll want to > sit back and use other people's tools. :) but those > are just the books! > There is so much for a programmer to do in > bioinformatics that books just > can't touch. > > Ah, but one or two more books. :) If you're of a > mathematical bent, you may > want to at least check out of the library Eddy's > book "Biological Sequence > Analysis" by Durbin, Eddy, Krogh and Mitchison. > There are several new > bioinformatics books out there that have just come > out (search > "bioinformatics" on Amazon.com), though from what > I've seen they're on the > === message truncated === ____________________________________________________________ Do You Yahoo!? Get your free @yahoo.co.in address at http://mail.yahoo.co.in From mtzitzib at hotmail.com Thu Feb 15 04:08:30 2001 From: mtzitzib at hotmail.com (Maria Tzitzibasi) Date: Thu, 15 Feb 2001 09:08:30 -0000 Subject: [BiO BB] (no subject) Message-ID: An HTML attachment was scrubbed... URL: From idoerg at cc.huji.ac.il Thu Feb 15 04:45:00 2001 From: idoerg at cc.huji.ac.il (Iddo Friedberg) Date: Thu, 15 Feb 2001 11:45:00 +0200 (GMT+0200) Subject: [BiO BB] PDB sequence --> coding sequence In-Reply-To: <200102150934.EAA21080@www.bioinformatics.org> Message-ID: Hi all, (Question originally posted to the "Ask the Open Lab" forum. I'm reposting it here, hopefully something will arise). Does anybody know of some way to get the coding sequence given a sequence from PDB? As you may very well know, PDB sequences are usually partial, fragmented versions of the actual protein sequence. Sometimes with mutations inserts (OK, so I cannot get the coding sequence for mutation inserts, for obvious reasons). Collating this data via automatic means seems rather cumbersome. Any help, including pointers to an appropriate database, scripts repository, or any kind of forum with people who might be able to answer this would be useful. Thanks, Iddo Friedberg -- Iddo Friedberg | Tel: +972-2-6758647 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ From Deanne.Taylor at pfizer.com Thu Feb 15 09:10:29 2001 From: Deanne.Taylor at pfizer.com (Taylor, Deanne) Date: Thu, 15 Feb 2001 09:10:29 -0500 Subject: [BiO BB] PDB sequence --> coding sequence Message-ID: <35AAFCDE1F5FD4118B7F00508B60945C03164289@aadino.research.aa.wl.com> Iddo: Apologies if you already know some of this stuff (in advance). :) My suggestion is to use tblastn. You can search with your fragment at BLAST at NCBI; though your fragment may have several intronic sequences removed, sometimes BLAST can match parts of your protein to different DNA regions. There are several flavors of BLAST available but you want tblastn. Go to http://www.ncbi.nlm.nih.gov/BLAST/ and select "Protein query -- translated db [tblastn]" under the Translated BLAST searches. tblastn is for comparing a protein query against a nucleic acid database (the nucleic acid database sequences are translated into all six reading frames and then compared to the protein query sequence). If tblastn doesn't work for you, write back, I might have links to various other things that might be of use, but none so convenient as a web interface. :) A good place to look for that kind of thing yourself is Pedro's bioinformatics tool list: http://www.public.iastate.edu/~pedro/rt_1.html Good luck! Deanne -----Original Message----- From: Iddo Friedberg [mailto:idoerg at cc.huji.ac.il] Sent: Thursday, February 15, 2001 4:45 AM To: bio_bulletin_board at bioinformatics.org Subject: [BiO BB] PDB sequence --> coding sequence Hi all, (Question originally posted to the "Ask the Open Lab" forum. I'm reposting it here, hopefully something will arise). Does anybody know of some way to get the coding sequence given a sequence from PDB? As you may very well know, PDB sequences are usually partial, fragmented versions of the actual protein sequence. Sometimes with mutations inserts (OK, so I cannot get the coding sequence for mutation inserts, for obvious reasons). Collating this data via automatic means seems rather cumbersome. Any help, including pointers to an appropriate database, scripts repository, or any kind of forum with people who might be able to answer this would be useful. Thanks, Iddo Friedberg -- Iddo Friedberg | Tel: +972-2-6758647 Dept. of Molecular Genetics and Biotechnology | Fax: +972-2-6757308 The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il POB 12272, Jerusalem 91120 | Israel | http://bioinfo.md.huji.ac.il/marg/people-home/iddo/ _______________________________________________ BIO_Bulletin_Board maillist - BIO_Bulletin_Board at bioinformatics.org http://bioinformatics.org/mailman/listinfo/bio_bulletin_board