From kikimaeda at gmail.com Mon Jun 2 07:40:00 2008 From: kikimaeda at gmail.com (daniel maeda) Date: Mon, 2 Jun 2008 13:40:00 +0200 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: References: Message-ID: hi i think you could also ask/consult Prof.Yamanaka because he published on these TFs in his papers so he must have the target sequences. On 27/05/2008, Jinyan Huang wrote: > > I want to get the Transcription Factor target sequences. They are > Oct4?Sox2?cMyc?Klf4?Nanog?Lin28. > Is there such free database? Or should I just search it one by one > from the literature? > > > -- > Best regards, > Jinyan Huang (ekeen) > School of Life Sciences and Technology, 1302 Room > Tongji University > Siping Road 1239, Shanghai 200092 > P.R. China > Tel :0086-21-65981041 > Msn: hiekeen at hotmail.com > eMail: hiekeen at gmail.com > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Daniel Maeda MCB Student, University of Heidelberg. Einzelzimmer Nr. 107-01-U1-3 im Studentenwohneim Im Neuenheimer Feld 687 69120 Heidelberg. Germany Tel:+491756407545 From hiekeen at gmail.com Mon Jun 2 12:18:33 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Tue, 3 Jun 2008 00:18:33 +0800 Subject: [BiO BB] How to get the special Transcription Factor target sequences? In-Reply-To: <89c69d9b0805302108u13321a9dy331666b151df628b@mail.gmail.com> References: <701a2c50805271003r2dd3945cv67f3f28d1b10ef54@mail.gmail.com> <3400.66.44.122.59.1211996127.squirrel@webmail.sibs.ac.cn> <89c69d9b0805302108u13321a9dy331666b151df628b@mail.gmail.com> Message-ID: Yes, I can find binding sites Oct4, Sox2 and c-Myc. But factors of lin28, Klf4 and nanog cannot be found in this database. On Sat, May 31, 2008 at 12:08 PM, Alexander Kel wrote: > Hi all, > > To use the free public TRANSFAC > please, click at: > http://www.gene-regulation.com/pub/databases.html > > on the third item in the list: > "Search TRANSFAC Public" > http://www.gene-regulation.com/cgi-bin/pub/databases/transfac/search.cgi > > Sorry, for the confusion. Our sales and marketing made a good > effort to put the Transfac professional at the top of the list :) > But still the public version is available. > > Alexander > > > > > On Thu, May 29, 2008 at 3:23 AM, Jinyan Huang wrote: >> Thank you very much for your suggestion. >> >> It is easy to registrate on gene-regulation.com. But when I browse the >> TRANSFAC database, it links to http://www.biobase-international.com/. >> For a free trial, it must finish a registration form. It is hard to >> pass this registration form. It is like this >> http://www.biobase-international.com/pages/index.php?id=456. >> >> >> In JARSPAR I can not find the factors which I interested >> >> no profiles in JASPAR satisfies search criteria >> >> >> >> 2008/5/29 lichunjiang : >>> >>> >>> Really? I registrated for gene-regulation.com a couple of years ago, it is >>> quite easy.?It does not make sense that you can not register. Or you >>> should just write to the service to fix the problem. >>> >>> Actually, >>> it is free to use a reduced version. For the full professional version, >>> you need to pay. >>> >>> Besides Transfac, I recommend another >>> database: JARSPAR available at http://jaspar.genereg.net/.?It is >>> totally free to use. >>> Hope this help. >>> Good luck! >>> >>> >>> >>>> It seems it is hard to pass the registration. >>>> >>>> 2008/5/28 J Greenbaum : >>>>> The >>> Transfac database (www.gene-regulation.com/pub/databases.html) >>>>> should have what you are looking for... >>>>> >>>>> Jason Greenbaum >>>>> Postdoctoral Fellow >>>>> >>> La Jolla Institute for Allergy & Immunology >>>>> >>>>> 2008/5/27 Jinyan Huang : >>>>>> I want to get the Transcription Factor target sequences. >>> They are >>>>>> >>> Oct4 $B!$ (BSox2 $B!$ (BcMyc $B!$ (BKlf4 $B!$ (BNanog $B!$ (BLin28. >>>>>> Is there such free database? Or should I just search it one >>> by one >>>>>> from the literature? >>>>>> >>>>>> >>>>>> -- >>>>>> Best regards, >>>>>> Jinyan Huang (ekeen) >>>>>> School of Life >>> Sciences and Technology, 1302 Room >>>>>> Tongji University >>>>>> Siping Road 1239, Shanghai 200092 >>>>>> P.R. >>> China >>>>>> Tel :0086-21-65981041 >>>>>> Msn: >>> hiekeen at hotmail.com >>>>>> eMail: hiekeen at gmail.com >>>>>> >>>>>> >>> _______________________________________________ >>>>>> BBB >>> mailing list >>>>>> BBB at bioinformatics.org >>>>>> >>> http://www.bioinformatics.org/mailman/listinfo/bbb >>>>>> >>>>> >>>>> >>> _______________________________________________ >>>>> BBB mailing >>> list >>>>> BBB at bioinformatics.org >>>>> >>> http://www.bioinformatics.org/mailman/listinfo/bbb >>>>> >>>> >>> >>>> >>>> >>>> -- >>>> Best regards, >>>> >>> Jinyan Huang (ekeen) >>>> School of Life Sciences and Technology, >>> 1302 Room >>>> Tongji University >>>> Siping Road 1239, Shanghai >>> 200092 >>>> P.R. China >>>> Tel :0086-21-65981041 >>>> Msn: >>> hiekeen at hotmail.com >>>> eMail: hiekeen at gmail.com >>>> >>>> _______________________________________________ >>>> BBB >>> mailing list >>>> BBB at bioinformatics.org >>>> >>> http://www.bioinformatics.org/mailman/listinfo/bbb >>>> >>>> >>> >>> >>> >>> -- >>> lichunjiang at sibs.ac.cn >>> Institute of >>> Biochemistry and Cell Biology, >>> Shanghai Institutes for Biological >>> Sciences, >>> Chinese Academy of Sciences >>> >>> _______________________________________________ >>> BBB mailing list >>> BBB at bioinformatics.org >>> http://www.bioinformatics.org/mailman/listinfo/bbb >>> >>> >> >> >> >> -- >> Best regards, >> Jinyan Huang (ekeen) >> School of Life Sciences and Technology, 1302 Room >> Tongji University >> Siping Road 1239, Shanghai 200092 >> P.R. China >> Tel :0086-21-65981041 >> Msn: hiekeen at hotmail.com >> eMail: hiekeen at gmail.com >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > > -- > Alexander Kel, PhD > SVP R&D > BIOBASE GmbH, > Halchtersche Strasse 33 > D-38304 Wolfenbuettel > Phone: +49 (0) 5331-8584-41 > Fax: +49 (0) 5331-8584-70 > www.biobase.de > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From jeff at bioinformatics.org Mon Jun 2 15:48:55 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 02 Jun 2008 15:48:55 -0400 Subject: [BiO BB] April-May '08 issue of the Bioinformatics.Org Newsletter is now available Message-ID: <48444EA7.4020609@bioinformatics.org> The newsletter includes some of the best of our various online forums and details some of our internal (and external) activities. IN THIS ISSUE: - Franklin Award wrap-up - New to the Board of Directors: Prashanth Suravajhala - Unveiling Pipet (part three) - Job search highlight - Upcoming events URL: http://www.bioinformatics.org/newsletter/ Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From mashranga at yahoo.com Tue Jun 3 06:50:24 2008 From: mashranga at yahoo.com (Mohammad Tanvir Ahamed) Date: Tue, 3 Jun 2008 03:50:24 -0700 (PDT) Subject: [BiO BB] Need Scholarship Message-ID: <800353.20994.qm@web53807.mail.re2.yahoo.com> I am Tanvir Ahamed and styding M.Sc in Bioinformatics at Chalmers University of Technology , Sweden. Now i want to get a scholarship. If anyone please let me know how can i manage it, it will be very helpfull for me. Tanvir Ahamed From jeff at bioinformatics.org Tue Jun 3 16:44:18 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Tue, 03 Jun 2008 16:44:18 -0400 Subject: [BiO BB] CfP: Bioinformatics to Systems Biology 2008 Message-ID: <4845AD22.1070202@bioinformatics.org> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- Call for Presentations/Participation Bioinformatics to Systems Biology 2008 Online at Bioinformatics.Org July 14, 2008 http://wiki.bioinformatics.org/Bioinformatics_to_Systems_Biology_2008 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- This year's conference, Bioinformatics to Systems Biology 2008 (BSB '08), is aimed at students and those in the research community who fall under broader disciplines of bioinformatics and systems biology. The BSB '08 conference will include invited keynote talks within subdisciplines of these two exciting fields. In addition to keynote addresses, individuals are invited to submit abstracts for presentation as talks in concurrent sessions, or as posters. Ample time will be set aside for discussion during the presentation of participants. We invite you to submit your original and unpublished contribution for presentation at this virtual conference from all subfields of bioinformatics and systems biology. Abstracts submitted would be evaluated by the program committee through a three-tier reviewing process and the three selected abstracts would be chosen for an oral talk. The rest of the selected submission would, however be printed in our conference proceedings. We are looking forward to publish in one of the open access journals as well. We also encourage researchers to submit proposed works or works in progress. Please send your (maxmimum two-page) abstracts containing NOT more than 500 words with sub-heads: motivation, introduction and review of literature, methods/tools employed, results and discussion, conclusions, future aviations, references, to bsb08 at bioinformatics.org not later than July 5, 2008, 1500hrs GMT. The figures and tables, if any, should be clear and in-line with the particular sub-heads. The authors must also declare any competing interests. Bioinformatics.Org appreciates if authors also declare usage of open access of their submissions. Registration is now open! http://wiki.bioinformatics.org/Bioinformatics_to_Systems_Biology_2008 From psb-bnas at mit.edu Tue Jun 3 18:01:35 2008 From: psb-bnas at mit.edu (PSB-BNAS) Date: Tue, 3 Jun 2008 18:01:35 -0400 Subject: [BiO BB] Fwd: PSB 2009 session on "Biomolecular Networks: From Analysis to Synthesis" In-Reply-To: <4845BEDB.4000802@mit.edu> References: <4845BEDB.4000802@mit.edu> Message-ID: Call for Papers BIOMOLECULAR NETWORKS: FROM ANALYSIS TO SYNTHESIS A Pacific Symposium on Biocomputing 2009 session January 5-9, 2009, Fairmont Orchid, The Big Island of Hawaii Paper deadline July 14, 2008 Acceptance notification September 8, 2008 PSB Session and Tutorials January 5-9, 2009 Questions? psb-bnas at mit.edu Session Topics Technology, capable of designing cellular systems for specific functions and applications, has revolutionized molecular biology via the new area of synthetic biology- which focuses on design rather than analysis. There have been numerous recent advancements in synthesizing biological networks in academia as well as the corporate world. At the same time, the field still must overcome several challenges. This session aims to introduce novel engineering and other mathematical / computational methods that are successfully translated to yield significant biological applications. Another goal is to promote communication and collaboration of scientists from different arenas through this session. Papers within the following areas of design and synthesis of networks are encouraged: synthetic biology networks, bio-knowledge networks, and general mathematical/computational methods for network design/synthesis. Some of the objectives of this session include: 1. Emphasize the guiding role that computational methods should play in the design/synthesis of biological networks. 2. Create a new paradigm whereby biocomputing researchers can take more active, leading role in synthetic biology. 3. Promote communication and collaboration by scientists from other areas, especially from mathematics, engineering, physics, biological, and medical communities. 4. Apply novel network-related methods from engineering and applied mathematics (e.g. information theory, game theory) from the last couple of years to biological network design and synthesis. Paper Submission Considering the popularity of biological network analysis, this PSB session was developed to have a special focus on design and synthesis of biological networks in order to encourage the research in this new area. This session deals with both molecular networks (e.g. interactions, regulation) and supporting knowledge representation networks. Both the biocomputing and biological community could benefit from exchanges of ideas and this could open up new research venues. This call for papers seeks original, high quality manuscripts which are not submitted or published elsewhere. PSB also has a history of generous travel support. Please see submission details at: http://psb.stanford.edu/cfp-biomole.htm Session Co-chairs: Gil Alterovitz, Harvard/MIT Judith A. Blake, The Jackson Laboratory Drew Endy, MIT Marco F. Ramoni,Harvard/MIT From me.lixue at gmail.com Wed Jun 4 12:12:00 2008 From: me.lixue at gmail.com (Xue Li) Date: Wed, 4 Jun 2008 11:12:00 -0500 Subject: [BiO BB] how to compare biological distance between four proteins Message-ID: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> Hello all, I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A Only 1RZO:C, 1UQ5:A and 1UQ4:A have Uniprot accession No. 1RZO:C is P06750 1UQ5:A and 1UQ4:A are P02879 I am interested in comparing biological distance of 1AAI:A with the other three. Would some one please tell me how to do that? Thanks a lot. -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From idoerg at gmail.com Wed Jun 4 16:30:14 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Wed, 4 Jun 2008 13:30:14 -0700 Subject: [BiO BB] how to compare biological distance between four proteins In-Reply-To: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> References: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> Message-ID: What is "Biological distance"? On Wed, Jun 4, 2008 at 9:12 AM, Xue Li wrote: > Hello all, > > I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A > > Only 1RZO:C, 1UQ5:A and 1UQ4:A have Uniprot accession No. > > 1RZO:C is P06750 > 1UQ5:A and 1UQ4:A are P02879 > > I am interested in comparing biological distance of 1AAI:A with the other > three. Would some one please tell me how to do that? > > Thanks a lot. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Iddo Friedberg, Ph.D. CALIT2, mail code 0440 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0440, USA T: +1 (858) 534-0570 T: +1 (858) 646-3100 x3516 http://iddo-friedberg.org From me.lixue at gmail.com Wed Jun 4 16:37:27 2008 From: me.lixue at gmail.com (Xue Li) Date: Wed, 4 Jun 2008 15:37:27 -0500 Subject: [BiO BB] how to compare biological distance between four proteins In-Reply-To: References: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> Message-ID: <62ed16460806041337s652dca45s7274d50942225483@mail.gmail.com> Sorry for the confusion. By "Biological distance" I mean functional similarity. Thanks. Li On Wed, Jun 4, 2008 at 3:30 PM, Iddo Friedberg wrote: > What is "Biological distance"? > > On Wed, Jun 4, 2008 at 9:12 AM, Xue Li wrote: > > > Hello all, > > > > I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A > > > > Only 1RZO:C, 1UQ5:A and 1UQ4:A have Uniprot accession No. > > > > 1RZO:C is P06750 > > 1UQ5:A and 1UQ4:A are P02879 > > > > I am interested in comparing biological distance of 1AAI:A with the other > > three. Would some one please tell me how to do that? > > > > Thanks a lot. > > > > -- > > Xue, Li > > Bioinformatics and Computational Biology program @ ISU > > Ames, IA 50010 > > 515-450-7183 > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > > Iddo Friedberg, Ph.D. > CALIT2, mail code 0440 > University of California, San Diego > 9500 Gilman Drive > La Jolla, CA 92093-0440, USA > T: +1 (858) 534-0570 > T: +1 (858) 646-3100 x3516 > http://iddo-friedberg.org > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From christoph.gille at charite.de Wed Jun 4 17:21:02 2008 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Wed, 4 Jun 2008 23:21:02 +0200 (CEST) Subject: [BiO BB] how to compare biological distance between four proteins In-Reply-To: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> References: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> Message-ID: <62123.84.189.196.245.1212614462.squirrel@webmail.charite.de> I could not find 1AAI in http://www.ebi.ac.uk/pdbsum/ Is it mistyped? Anyway click http://www.charite.de/bioinf/strap/ce.php?align=PDB%3A1aai%3AA+PDB%3A1rzo%3AC+PDB%3A1uq5%3AA+PDB%3A1uq4%3AA Click the tool button "Op-tions" at the bottom and activate check-box "Full functionality" to activate the menu-bar. Menu-bar->Analyze->Compare proteins You could select either rmsd-value or TM-align score or CE-score or clustalw-score. Is it what you need? > Hello all, > > I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A > > Only 1RZO:C, 1UQ5:A and 1UQ4:A have Uniprot accession No. > > 1RZO:C is P06750 > 1UQ5:A and 1UQ4:A are P02879 > > I am interested in comparing biological distance of 1AAI:A with the other > three. Would some one please tell me how to do that? > > Thanks a lot. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From pfern at igc.gulbenkian.pt Thu Jun 5 02:00:43 2008 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Thu, 05 Jun 2008 07:00:43 +0100 Subject: [BiO BB] how to compare biological distance between four proteins Message-ID: <1212645643.4847810b6f94e@webmail.igc.gulbenkian.pt> Hi Xue-Li, There is no universal measurement of biological distance. There is controversy on the use of the term itself. Furthermore, when you "measure" something, you want your "measurement" to be comparable to others, so there is a need too know what we are talking about. For example if you do such a "measurement" on your four proteins today, you may want to compare your present "measurement" with "measurements" that you take tomorrow with another four proteins. Or another 500... A generalized concept of "distance" may be applied to evaluate similarity. In doing that you might be interested in conservation of motifs in proteins, so you might be interested in finding out what is conderved to start with. And in doing that you might be willing to consider similarity where non-silent mutations might have been involved. You may want to use a widespread multiple sequence alignment program. The simple way is to use CLUSTALW to get a multiple sequence alignment. This program has a bunch of parameters that can be used at their default value, but the careful user would look for ways of using these parameter to better adapt to a concrete biological situation. If ou use CLUSTALW you should state which parameters you use at each time. And that will depend on the concrete problem that you want to address. For example the matrix that is used to encode for mutation rates should relect the problem. It may be not be indifferent if you are studying proteins from mammals or procariots or plants! It may be good to play with more parameters and tell the program if you are aligning very dissimilar or very similar proteins. But there is no harm in using CLUSTALW with all the defaults and see what happens, provided that you know that you shuld not use the output without thinking before stating things about "distances". CLUSTALW outputs distances in the form of a tree file. Several formats are commonly availale for this. Check with the documentation on the way it is calculated and the possible further use of these distances. As you may have undertood by now, getting these numbers is only the beginning, the tip of the iceberg. And, mind you, if you just want to judge similarity you may opt for not using the term "distance" in the firt place! God luck Pedro -- Pedro Fernandes Instituto Gulbenkian de Ci?ncia Apartado 14 2781 OEIRAS PORTUGAL From pfern at igc.gulbenkian.pt Thu Jun 5 09:52:35 2008 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Thu, 05 Jun 2008 14:52:35 +0100 Subject: [BiO BB] how to compare biological distance between four proteins In-Reply-To: <62ed16460806041337s652dca45s7274d50942225483@mail.gmail.com> References: <62ed16460806040912q5ace3548q4d4e102b0fe1059e@mail.gmail.com> <62ed16460806041337s652dca45s7274d50942225483@mail.gmail.com> Message-ID: <1212673955.4847efa3dd3bd@webmail.igc.gulbenkian.pt> Hello again If you are looking for (known) functional properties you should use multiple alignments tuned so that you align motifs that you know that are related with known functions better than other parts of the protein sequences. You may know those motifs, because you may know protein domains or motifs that are associated with each function. You may also generate motifs for that purpose, artificially. finally, you may work on the conservation and select the bits of sequence that may have had a common ancestor where that particular function was found. Pedro -- Pedro Fernandes Centro Portugu?s de Bioinform?tica Instituto Gulbenkian de Ci?ncia Apartado 14 2781 OEIRAS PORTUGAL ----------------------------------------------------------- CONFIDENCIAL. Esta mensagem e os ficheiros eventualmente anexos s?o confidenciais. Se tiver recebido esta mensagem por engano, agradecemos que nos contacte imediatamente por e-mail ou pelo telefone +351 21 4407912 e que elimine a mensagem e ficheiros anexos sem os reproduzir. Quoting Xue Li : > Sorry for the confusion. > > By "Biological distance" I mean functional similarity. > > Thanks. > > Li > > On Wed, Jun 4, 2008 at 3:30 PM, Iddo Friedberg wrote: > > > What is "Biological distance"? > > > > On Wed, Jun 4, 2008 at 9:12 AM, Xue Li wrote: > > > > > Hello all, > > > > > > I have four proteins. 1AAI:A 1RZO:C 1UQ5:A 1UQ4:A > > > > > > Only 1RZO:C, 1UQ5:A and 1UQ4:A have Uniprot accession No. > > > > > > 1RZO:C is P06750 > > > 1UQ5:A and 1UQ4:A are P02879 > > > > > > I am interested in comparing biological distance of 1AAI:A with the other > > > three. Would some one please tell me how to do that? > > > > > > Thanks a lot. > > > > > > -- > > > Xue, Li > > > Bioinformatics and Computational Biology program @ ISU > > > Ames, IA 50010 > > > 515-450-7183 > > > _______________________________________________ > > > BBB mailing list > > > BBB at bioinformatics.org > > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > > > > > > -- > > > > Iddo Friedberg, Ph.D. > > CALIT2, mail code 0440 > > University of California, San Diego > > 9500 Gilman Drive > > La Jolla, CA 92093-0440, USA > > T: +1 (858) 534-0570 > > T: +1 (858) 646-3100 x3516 > > http://iddo-friedberg.org > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From recomb-cg at engr.uconn.edu Fri Jun 6 22:23:39 2008 From: recomb-cg at engr.uconn.edu (RECOM-CG 08) Date: Fri, 6 Jun 2008 22:23:39 -0400 (EDT) Subject: [BiO BB] RECOMB-CG 6th Annual RECOMB Satellite Meeting on Comparative Genomics Message-ID: Dear Colleague, It is our pleasure to announce the Sixth Annual RECOMB Satellite Meeting on Comparative Genomics and issue this call for submissions. We are looking forward to another great meeting, this year in Paris, France. We have an exciting group of confirmed keynote speakers, and anticipate a vibrant series of "late breaking talks" selected from the paper and poster submissions. Please consider submitting your own work for papers, posters, and talks. Submission details can be found below and on the conference website: http://igm.univ-mlv.fr/RCG08 Best Regards, Craig Nelson & Stephane Vialette (PC Co-chairs) Jens Lagergren, Aoife McLysaght, & David Sankoff (Steering Committee) ============================================================== RECOMB-CG, 2008 October 13-15, 2008 Ecole Normale Sup?rieure, Paris, France http://igm.univ-mlv.fr/RCG08 CONFIRMED KEYNOTE SPEAKERS Olga Troyanskaya (Princeton University) Aviv Regev (Broad Institute) Trisha Wittkop (University of Michigan) Chris Ponting (University of Oxford) Laurent Duret (Universit? Claude Bernard) KEY DATES Paper submission deadline June 18, 2008 Notification of paper acceptance July 14, 2008 Final manuscript due July 24, 2008 Poster submission deadline September 22, 2008 Workshop October 13-15, 2008 CALL FOR PAPERS Papers should be submitted via the EasyChair system. Submissions must be received in electronic form by 11:59pm (Paris local time), June 16th, 2008. Submissions should be no longer than 12 single-spaced A4 pages with 1.25-inch margins all around, everything included (title, authors, addresses, abstract, references, figures, tables), in at least a 10-point font. An optional short appendix may contain details or additional data to be consulted at the discretion of the program committee. Note that authors of accepted papers will have to reformat them for the proceedings using the Springer LNCS style, which has even wider margins. It may save the authors' some work if this format is used from the outset. The submission must include the corresponding author's email address. Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to the conference, and for the entire review period, the paper should not be under review by any other conference or scientific journal. Note that accepted papers will be considered as preliminary work, and may be submitted to a journal publication after notification of acceptance. Successful submissions will be invited for a 20-minute presentation, and the paper will be printed in the conference proceedings, which will be published by Springer in the "Lecture Notes in Bioinformatics" series. Address any questions to the program committee chairs: Craig E. Nelson (Craig.Nelson at uconn.edu) Stephane Vialette (vialette at univ-mlv.fr) THEME AND SCOPE Rapid DNA sequencing technologies have fueled an explosion in genome level data. RECOMB-CG is devoted to the development and utilization of computational methods for the comparative exploration of genome structure, function, and evolution. Both theoretical and applied contributions are welcome, and papers that combine new techniques with new knowledge derived from their application are highly encouraged. Submissions should include genome wide analyses informed by comparative data. Topics of interest include but are not limited to: Algorithms for comparative genomics Genome rearrangements Ancestral genome reconstruction Multiple genome alignment Genome sequence comparison Modeling genome evolution Identification, classification, and evolution of non-coding motifs Comparative genomics for genome annotation Gene and genome duplication Evolution of gene families Identification of highly conserved and rapidly evolving sequences Gene tree reconciliation Comparative genomics and epigenetics Comparative genomics and proteomics Comparative genomics and gene expression Comparative genomics and adaptation CONFERENCE CHAIRS Craig E. Nelson (Molecular & Cell Biology - Univ. of Connecticut, USA) Stephane Vialette (IGM - Univ. Paris-Est, France) STEERING COMMITTEE Jens Lagergren (Stockholm Bioinformatics Centre and CSC, KTH, Sweden) Aoife McLysaght (University of Dublin, Ireland) David Sankoff (University of Ottawa, Canada) PROGRAM COMMITTEE Lars Arvestad (Royal Institute of Technology, Sweden) Veronique Barriel (Museum national d'histoire naturelle, France) Anne Bergeron (Universite du Quebec a Montreal, Canada) Guillaume Blin (Universite Paris-Est, France) Guillaume Bourque (Genome Institute of Singapore, Singapore) Jeremy Buhler (Washington University in Saint Louis, USA) Pierre Capy (Universite Paris-Sud, France) Cedric Chauve (Simon Fraser University, Canada) Avril Coghlan (Sanger Institute, UK) Miklos Csuros (Universite de Montreal, Canada) Aaron Darling (University of Queensland, Australia) Bernard Dujon (Institut Pasteur, France) Dannie Durand (Carnegie Mellon University, USA) Nadia El-Mabrouk (Universite de Montreal, Canada) Niklas Eriksen (Goteborg University, Sweden) Guillaume Fertin (Universite de Nantes, France) Olivier Gascuel (Universite de Montpellier II, France) Henri Grosjean (Universite Paris-Sud, France) Matthew Hahn (Indiana University, USA) Tao Jiang (University of California - Riverside, USA) Jens Lagergren (Stockholm Bioinformatics Centre and CSC, KTH, Sweden) Emmanuelle Lerat (Universite Claude Bernard, France) Aoife McLysaght (University of Dublin, Ireland) Bernard Moret (Ecole Polytechnique Federale de Lausanne, Switzerland) Craig Nelson (Co-Chair, University of Connecticut, USA) Rasmus Nielsen (University of Copenhagen, Denmark) Michal Ozery-Flato (University of Tel-Aviv, Israel) Pierre Pontarotti (Universite de Provence, France) Eduardo Rocha (Universite Paris 6 et Institut Pasteur, France) Hugues Roest-Crollius (Ecole Normale Superieure, France) Antonis Rokas (Vanderbilt University, USA) Marie-France Sagot (INRIA Rh?ne-Alpes, France) David Sankoff (University of Ottawa, Canada) Cathal Seoighe (University of Cape Town, South Africa) Jens Stoye (Bielefeld University, Germany) Chuan-Yi Tang (National Tsing Hua University, Taiwan) Eric Tannier (INRIA Rh?ne-Alpes, France) Glenn Tesler (University of California - San Diego, USA) Stephane Vialette (Co-Chair, Universite Paris-Est, France) Louxin Zhang (National University of Singapore, Singapore) LOCAL ORGANIZING COMMITTEE Severine Berard (Univiversite de Montpellier II, France) Guillaume Blin (Univiversite Paris-Est, France) Maxime Crochemore (Univiversite Paris-Est, France) Hugues Roest Crollius (Ecole Normale Superieure, France) Guillaume Fertin (Univiversite de Nantes, France) Eric Tannier (INRIA Rh?ne-Alpes, France) Jean-Stephane Varre (INRIA Futurs - Univiversite de Lille, France) Stephane Vialette (Universite Paris-Est, France) REGISTRATION Registration will be available on the conference website. ============================================================== Your RECOMB-CG subscription preferences can be updated at http://dna.engr.uconn.edu/mailman/listinfo/recomb-cg -------------- next part -------------- _______________________________________________ RECOMB-CG mailing list RECOMB-CG at dna.engr.uconn.edu http://dna.engr.uconn.edu/mailman/listinfo/recomb-cg From kanzure at gmail.com Sat Jun 7 11:51:22 2008 From: kanzure at gmail.com (Bryan Bishop) Date: Sat, 7 Jun 2008 10:51:22 -0500 Subject: [BiO BB] DIY Biotech Book Message-ID: <200806071051.23258.kanzure@gmail.com> Hey all, The biobarcamp guys and others are planning to do a do-it-yourself biotech book. The idea is to make a book that introduces and includes information on how to make and use the biotech equipment, the do-it-yourself scene, and so on. There's already significant content in the biotech toolkit ( http://biohack.sf.net/ ) *however* there's also tons of information from other communities that really needs to be integrated into something new -- a book -- so I'm sending out this email as notification of where everybody is. It looks like nobody is keeping notes on it yet, so I'm taking the initative and organizing everything here: http://heybryan.org/mediawiki/index.php/Book Feel free to edit it ruthlessly, copy it to another wiki, whatever. The content for the book itself should be up on a wiki, so feel free to link over to new pages with content dumps of related interest. There's going to be a lot of contributions, but we can sort through it in the end and discuss what we want to finally include and what not and so on. I'm also emailing this to a number of mailing lists. Mailing lists are limited for large collaborative projects like this where we don't have everyone on the same page and copying emails between too many mailing lists has this tendency to be a not-so-good of an idea. So, to provide a medium to more quickly organize people from different groups, I'm hanging out on IRC in #hplusroadmap on freenode and hope others will join me. There's a good number of contributors interested in this project there (>10 normally). There's also #biology, #bioinformatics, ##neuroscience, and a good number of other communities on freenode that we can dive into. Here's how you can access it: http://irchelp.org/ http://freenode.net/ irc://irc.freenode.net/#hplusroadmap Anybody using Firefox can use Chatzilla. Window users can use mIRC or something. And people on linux can apt-cache search IRC | grep IRC and get something that looks good. I'm also going to propose a 'cycle' of contributions to follow so that we have somewhat of a pulse that can beat out content. Wikipedia has a community pump, for example. There's a few options over at twitter, but in general, I think we'll get a pump going (aggregator) through IRC and then decide on twitter or whatever. Twitter is down all the time, so somebody else might have a better idea than I. In the mean time: http://twitter.com/biotecher http://pimm.wordpress.com/2008/04/14/follow-biotecher-a-solution-to-find-all-biotwitters-in-1-place/ http://twitter.com/attilacsordas http://twitter.com/kanzure http://twitter.com/mndoci I'm emailing this over to a lot of different communities into this sort of thing -- the neuralensemble group that focuses on the computational neuro side of biotech, the longevity groups, etc. All of these people are awesome and have good ideas to contribute, so I'm hoping some of them will click on the biotecher twitter, show up on the IRC discussions, and end up making an even more amazing resource for individuals. - Bryan ---------- Forwarded Message ---------- Subject: Re: [BioBarCamp] BioBarCamp topic/session suggestions Date: Saturday 07 June 2008 From: Bryan Bishop To: biobarcamp at googlegroups.com On Tuesday 03 June 2008, Attila Csordas wrote: > Hi All, > > This will be a lengthy email (sorry), but with good chance, it covers > a lot of topics that will be discussed at BBCAmp. The reason for that > length is that I include the Tentative Table of Contents of the so > called *BioTech Geek Guide* as I would like to organize the closing > session of the BBCamp with Deepak and Ricardo with the interactive > participation of you all. Let me explain: > > The *Biotech Geek Guide* is also an > ideait-folks-book-and-publish-it/>fed by a Twitter stream, just like the > BBCamp idea. Deepak complained about > the tech world's ignorance about health & genetics (a recurrent > theme) and then I suggested to write/edit/compile a biotech, biology > book for IT folks specially and publish it as an O'Reilly book. > O'Reilly Books have the fame of being the definitive guides, intros, > manuals in their technolgical fields. Ricardo came into the > conversation too and 10 minutes later I emailed Tim O'Reilly with the > suggestion and got almost instantly a very positive answer back > followed by a detailed Proposal Guidelines that needs to be filled > out to set up a schedule in order to get a final Yes or No answer to > the publishing of the book. So we started to work (just a little in > the lack of time) on it and I copy here what we've done basically the > *Book Outline/Tentative Table of Contents*. The concept of the book > later transformed into the *Biotech Geek Guide* which is too collect > every cool, major topic together that could be of interest for a > rookie/advanced biogeek, who is usually tech-savvy and biotech-savvy > too. I was talking with Deepak and others a few weeks ago about offering the Synthetic Biology Toolkit as a basis for the book. There's tons of content in the download and I think that it would be a good place to start. http://biohack.sf.net/ http://heybryan.org/mediawiki/ So the table contents, I would think, should focus mostly on (1) protocols, (2) equipment -- mostly improvised, (3) introduction to the online communities, including the broader world of bioinformatics, programming, open source communities, friendly people to talk to on the internet (seriously, an email address to me, Deepak, pimm, etc.), diybio.org groups, etc. The entire field is very quickly moving along, so it has to be a book that will not be dead in a few months (books aren't good for content like that). > And so we have an idea, an option to make a product (a book) out of > it, and define or delineate the knowledge-base and topic sensitivity > of current biotechnology, life sciences well tailored for IT people > but we lack an essential component that is behind every good animal > covered O'Reilly tech book: we lack the creative and critical > community and we need authors and commenters in the spirit of open > source and science. (That community also starts to form on FriendFeed Woah, I think we /do/ have that community. Check out the biohack.sf.net community. There's a good number of people on the mailing list. We just need to get them rallied up on a project. :-) > as *The Life > Scientists*room, > earlier form is a simply > Biotecher > registertion-to-find-all-biotwitters-in-1-place/>at Twitter.) > > But I think that the BioBarCamp could collect together exactly the > Community that is needed for the succession of that book and the > whole biogeek culture!!! The authorship, content and schedule is > totally open at that point (publishing an O'Reilly book is not about > money, really, at least I think so), I'd (and probably Deepak, if he > is interested) serve as a kind of main editor, and the more coauthors > and voices we have, the better the book will be. Let's make it on a wiki, instead of requiring it a BioBarCamp-only book. I don't know if BioBarCamp would be a good venue at which to write the book, but for rapid outlining (sit there on a wiki and have a live brainstorming session) it might prove an awesome mechanism. > So by copying the content suggestions here, I'd like to invite you > all to this hypothetical closing session and invite you to become > future O'Reilly authors to define the biogeek culture. (Disclaimer: I > am not an employee of O'Reilly Media, and if they say no I still > think that the concept of the book is good enough to publish it > elsewhere). To _define_ the biotecher culture? I don't know about that. That one is already in progress. For example, biopunk.org, the F/OSS communities, the typical lab culture. > 1. *All about bio* (introduction to the book). In the > introduction we will discuss the the origins of biotechnology and how > the field has evolved over the past 25 years? As biotechnology has That's a pretty challenging part. Maybe we could start by looking over at wikibooks and see if there's anything already written that we might import. There's a lot of important people to mention from the field of bio and biotech and so on, so we need somebody pretty knowledgable and able to integrate all of the information together, showing the broader vision that people started out with (or acquired), and then integrating it all back together to make sense. I think this could be done if we ruthlessly recursively read Wikipedia for the broad overview aspects, but then we need to reinterpret in light of (1) actual research articles (references to open access papers, etc.), and (2) an interpretation in terms of the do-it-yourself culture. > evolved, it has had a significant impact on the world around us, from > how we approach problems to how we try and cure disease, to the I think it's important to emphasize just how awesome disease curing can be. I wasn't aware of the World Health Organization's attempt to cure polio via a world-wide campaign until a few years ago. That was a terribly massive medical front that I doubt can be emphasized enough. And what would happen if people were able to do that on their own? Hrm. > environment and even to DIY hackery. The world of biotechnology is > also increasingly moving towards a systems level approach, as begin > to look at our bodies as interconnected, complex machines, changing > the way we try and cure diseases. We will also propose that biology > is the ultimate information science and lay the grounds for later > discussions on the data challenges and the information that can be > gleaned > 1. the biological mindset > 2. biotechnology in general > 2. biology basics In this chapter we provide a brief introduction > of the building blocks of biology. Here we go a little beyond what > you might find in the mainstream media and tell you about how we > function and highlight the complexity of human biology > 1. The building blocks (DNA, RNA, protein, organelles, membranes, > extracellular matrix, tissues, organs, body). *Do we need > anything else here? Don't want to make it too technical.* So, a list of general componentry that people can investigate in trying to make their projects a reality. Not just "building blocks of life", but 'parts and tools that you can use to do cool stuff'. > 3. methods - I suspect that including a CD of protocols wouldn't be a bad idea. We could start with protocols-online and OpenWetWare. In fact, if there's going to be a CD, let's include the biohacking toolkit and the entire wiki output of major wikis like OWW, biodatabase.org, biohack, etc. And then we can probably also include the portions of Wikipedia that are relevant. This is critical. There's no way that we can talk about everything in a book that we all want to be published in a reasonable amount of time ... so a CD, plus the book as more of a creative 'index' (in discussion format) to the contents, might be a good idea. > 1. the lab The par excellence biologist of our time is an > experimental scientist working at the bench with different tools and > methods: DNA, RNA: > isolation, amplification, quantification, protein: western > blot, SDS PAGE, > antibodies immunocytochemistry organelle: isolation of > mitochondria, lysosomes (centrifuge), cell: in vitro cell culture > 2. Biology in silico http://heybryan.org/mediawiki/index.php/Computational_biology > 1. Bioinformatics http://bioinformatics.org/ > 2. Modeling and simulation http://heybryan.org/mediawiki/index.php/Computational_biology > 4. Postgenomic > 1. proteomics http://heybryan.org/mediawiki/index.php/List_of_bioinformatics_databases > 2. HapMap > 3. Protein Structure Initiative (Structural Genomics) CASP? > 5. Systems Biology Over the past few years, it has become http://sbml.org/ > apparent that the traditional reductionist approach to biology was > very limited. The human body is extremely complex, a function of > interconnected pathways and networks. In order to cure many > diseases, it becomes necessary to study the human body at a systems > level, getting a deep understanding of various pathways and networks. http://reactome.org/ > By combining large quantities of data, complex mathematical > modeling and advanced computer models, systems biologists are > developling predictive models of organisms and biological systems > which will not only help us develop better, more potent drugs, but > also develop new fuel sources, clean up the environment and > potentially hack the human body. 6. The future of biotech Re: future of biotech. George Church is supposedly making some incredibly cheap biotech equipment (polonator.org and so on); sequencing for everybody on the planet; do-it-yourself pharmacy; brain augmentation; etc. http://www.innerspacefoundation.org/ http://heybryan.org/recursion.html > 1. Next generation sequencing http://heybryan.org/mediawiki/index.php/DNA_sequencing Is pyrosequencing still next generation? There's also scanning tunneling microscopy for DNA (like ZS Genetics plans to be doing later this year). The STM setups technically don't cost much, but getting the reoslution needed to do nucleotide-by-nucleotide scanning, ehh. That gets tricky. See: http://heybryan.org/instrumentation/instru.html http://heybryan.org/graphene.html (sort of) > 2. Personal Genetics - Genomics http://polonator.org/ Also, the $0 genomics project. Community sequencing projects, brief notes on how to deploy something like that (run around with cotton swabs and baggies and refridgerators in a van), etc. Also, the prospects of viral gene therapy in relation to personal genomics; the prospects of downloading genes from the internet from "gene pools" (i.e., "hey, look at this!" blogs). > 3. stem cells-regenerative medicine (A) The chapter covers the > basic concepts: stem cell, uni-, mult-, pluripotency, embryonic, > adult, induced pluripotent, cancer stem cell, stem cell niche, tissue > regenerative potential, regenerative medicine. The biohacking toolkit includes some papers by Yamanaka re: iPS cells. I'm still looking into protocols for adult fibroblast extraction and colonies, but it's looking interesting. > 4. tissue engineering http://heybryan.org/mediawiki/index.php/Neuropod organotypical neural slices, also see the heart-in-a-jar and prospects of the brain-in-a-jar projects. Stem cell engineering too. Hrm. Ah, and most importantly, the in vitro meat stuff. http://heybryan.org/mediawiki/index.php/Meat_on_a_stick > 5. The biology of our age: the biology of aging Emphasis on how to do "anti-aging research" in your own home. http://sens.org/ http://grg.org/ has some people that we might want to contact (Coles? Aubrey?) > 6. synthetic biology* *Perhaps we can get Jason or someone to > do this. My preference is that we stick to non-famous people but > interview Drew and others extensively. http://syntheticbiology.org/ http://partsregistry.org/ http://biobricks.org/ http://biohack.sf.net/ http://diybio.org/ > 7. biotech DIY: set up your low budget lab at the backyard > The idea of doing biological experiments with current > biotechnological methods and conducting research projects at home is > very new. There are already many names in use referring to the same > concept: bioDIY, home biology, biotech DIY, garage biology. All you > people need is a short course > in biotech basics, a few thousands of dollars, some tinkering > capability, and enough spare time and space. The beautiful retro idea > of tinkering with > digital devices in a garage, conveyed by the > Makemagazine, can be extended to biotech > too, and some projects were already > published in Make backyard biology issue like the Home > Molecular Genetics including DNA isolation. By the way. There's a few projects out there (bioreactor project from the biohacking group) that are trying to make a completely biological setup for do-it-yourself biology experimentation. For example, in vitro DNA synthesis. http://heybryan.org/mediawiki/index.php/In_vitro_DNA_synthesizer And also having cells generate the proteins (T7, etc.) necessary to do transcription, or other various reactions that will be needed. This way, the entire kit is self-replicable except for the metal or plastic chasis. > 7. Applications > 1. industrial biotech Might want to mention something about 'industrial ecology' and the biosphere as another ecology and how this could all fit together productively for various interests. > 2. Drug Discovery > 8. The Web and biotech > 1. Google and biotech Google's interindustrial power reached > the biotech sphere through its investment into 23andME and backing > George Church's Personal Genome Project amongst others. While > personal genomics is > in the focus of Google's recent interest, its connection with > the biomedical > sector is much more complicated. Google Health > 2. Virtual medical education and web 2.0 in medicine Maybe the diybio.org guys would like to run some of those virtual educational seminars eventually. I've been holding weekly lectures on IRC on freenode in #hplusroadmap for a while now, but it's really just whenever people feel like showing up and pestering me about some awesome topics. Anybody is welcomed to join and contribute. :) - Bryan ________________________________________ http://heybryan.org/ ------------------------------------------------------- ________________________________________ http://heybryan.org/ From me.lixue at gmail.com Sat Jun 7 22:03:57 2008 From: me.lixue at gmail.com (Xue Li) Date: Sat, 7 Jun 2008 21:03:57 -0500 Subject: [BiO BB] what the difference between remediated pdb and pdb? Message-ID: <62ed16460806071903i3e1b1c2en57853d611b6ec83@mail.gmail.com> Hello all, >From remediated pdb web site http://remediation.wwpdb.org/index.html, I read "Updated references to databases and taxonomies and Resolved differences between chemical and macromolecular sequences". Does it mean that for some proteins they will have difference sequences in remediated pdb and ordinary pdb? Thanks. -- Xue, Li Bioinformatics and Computational Biology program @ ISU Ames, IA 50010 515-450-7183 From JFALLAH at modares.ac.ir Sun Jun 8 09:59:45 2008 From: JFALLAH at modares.ac.ir (jalil fallah mehrabadi) Date: Sun, 08 Jun 2008 17:29:45 +0330 Subject: [BiO BB] number of total genes Message-ID: To whom it my concern I was wondering if you would mind answering me how could I find the total number of genes for a eukaryot and prokaryotic cells in NCBI. I checked Map viewer , Genome , Genome project and Taxonomy in NCBI but unfortunately could not find it. thank you in advance Jalil Fallah Ph.D student of Medical Bacteriology Tarbiat Modares University Tehran , Iran From marchywka at hotmail.com Mon Jun 9 12:24:06 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Mon, 9 Jun 2008 12:24:06 -0400 Subject: [BiO BB] number of total genes In-Reply-To: References: Message-ID: > I was wondering if you would mind answering me how could I find the total > number of genes for a eukaryot and prokaryotic cells in NCBI. Do you really need to know the number of genes for something or are you asking a larger question about the structure of and interface to existing sequence data? Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Sun, 8 Jun 2008 17:29:45 +0330 > From: JFALLAH at modares.ac.ir > To: bbb at bioinformatics.org > Subject: [BiO BB] number of total genes > > To whom it my concern > > I was wondering if you would mind answering me how could I find the total > number of genes for a eukaryot and prokaryotic cells in NCBI. I checked Map > viewer , Genome , Genome project and Taxonomy in NCBI but unfortunately > could not find it. > > thank you in advance > Jalil Fallah > Ph.D student of Medical Bacteriology > Tarbiat Modares University > Tehran , Iran > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Instantly invite friends from Facebook and other social networks to join you on Windows Live? Messenger. https://www.invite2messenger.net/im/?source=TXT_EML_WLH_InviteFriends From roberto.mosca at embl-hamburg.de Mon Jun 9 12:45:40 2008 From: roberto.mosca at embl-hamburg.de (Roberto Mosca) Date: Mon, 9 Jun 2008 18:45:40 +0200 Subject: [BiO BB] what the difference between remediated pdb and pdb? In-Reply-To: <62ed16460806071903i3e1b1c2en57853d611b6ec83@mail.gmail.com> References: <62ed16460806071903i3e1b1c2en57853d611b6ec83@mail.gmail.com> Message-ID: <425343C3-DADB-498F-A937-A6CB2C9A6770@embl-hamburg.de> From the document: "3.5 Resolution macromolecular sequence conflicts Differences in entity sequence assignment between RCSB PDB and MSD-EBI have been resolved. Any remaining differences between the chemical sequence and the macromolecular sequence have also been resolved." I think that this refers only to the DBREF and SEQRES records in the file. Of course an alanine cannot become a valine or a tyrosine when going from the original to the remediated PDB. I'm not sure what kind of errors have been fixed but I think there could have been inconsistencies between the sequence reported in the SEQRES records and the sequence corresponding to the ATOM records in the PDb file itself. Roberto ............................................ Dr. Roberto Mosca EMBL c/o DESY Notkestr. 85 22607 Hamburg Germany Email: roberto.mosca at embl-hamburg.de Tel: +49 (0)40 89902 131 Web: http://www.embl-hamburg.de/~rmosca ............................................ On Jun 8, 2008, at 04:03, Xue Li wrote: > Hello all, > >> From remediated pdb web site http://remediation.wwpdb.org/ >> index.html, I read > "Updated references to databases and taxonomies and Resolved > differences > between chemical and macromolecular sequences". > > Does it mean that for some proteins they will have difference > sequences in > remediated pdb and ordinary pdb? > > Thanks. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From jforment at ibmcp.upv.es Mon Jun 9 13:43:21 2008 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Mon, 9 Jun 2008 19:43:21 +0200 Subject: [BiO BB] software for protein threading Message-ID: <1213033401.484d6bb98959d@webmail.upv.es> Hi, all... We are attempting to do a temptative functional annotation for EST-derived partial ORFs which didn't found an annotated similar sequence in BLAST searches. Could anyone suggest a software for automated fold recognition by threading in local computers? Thanks in advance, Javier. -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 FAX: +34-96-3877859 jforment at ibmcp.upv.es From marty.gollery at gmail.com Mon Jun 9 14:13:16 2008 From: marty.gollery at gmail.com (Martin Gollery) Date: Mon, 9 Jun 2008 11:13:16 -0700 Subject: [BiO BB] software for protein threading In-Reply-To: <1213033401.484d6bb98959d@webmail.upv.es> References: <1213033401.484d6bb98959d@webmail.upv.es> Message-ID: There are a number of them out there, Javier, but you might want to run them through something more comprehensive such as InterProScan first. Best Regards, Marty On Mon, Jun 9, 2008 at 10:43 AM, Javier Forment Millet wrote: > Hi, all... > > We are attempting to do a temptative functional annotation for EST-derived > partial ORFs which didn't found an annotated similar sequence in BLAST > searches. Could anyone suggest a software for automated fold recognition by > threading in local computers? > > Thanks in advance, > > Javier. > > > -- > Javier Forment Millet > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > jforment at ibmcp.upv.es > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- -- Martin Gollery Senior Bioinformatics Scientist TimeLogic- a Division of Active Motif 775-833-9113 880 Northwood Blvd. Suite 7 Incline Village, NV 89451 From JFALLAH at modares.ac.ir Tue Jun 10 03:38:55 2008 From: JFALLAH at modares.ac.ir (jalil fallah mehrabadi) Date: Tue, 10 Jun 2008 11:08:55 +0330 Subject: [BiO BB] number of total genes In-Reply-To: References: Message-ID: Dear all Really thanks for your reply. I need just the total number of some eukaryot and prokaryotic cells. Thanks again Jalil -----Original Message----- From: Mike Marchywka To: General Forum at Bioinformatics.Org Date: Mon, 9 Jun 2008 12:24:06 -0400 Subject: Re: [BiO BB] number of total genes > I was wondering if you would mind answering me how could I find the total > number of genes for a eukaryot and prokaryotic cells in NCBI. Do you really need to know the number of genes for something or are you asking a larger question about the structure of and interface to existing sequence data? Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Sun, 8 Jun 2008 17:29:45 +0330 > From: JFALLAH at modares.ac.ir > To: bbb at bioinformatics.org > Subject: [BiO BB] number of total genes > > To whom it my concern > > I was wondering if you would mind answering me how could I find the total > number of genes for a eukaryot and prokaryotic cells in NCBI. I checked Map > viewer , Genome , Genome project and Taxonomy in NCBI but unfortunately > could not find it. > > thank you in advance > Jalil Fallah > Ph.D student of Medical Bacteriology > Tarbiat Modares University > Tehran , Iran > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Instantly invite friends from Facebook and other social networks to join you on Windows Live? Messenger. https://www.invite2messenger.net/im/?source=TXT_EML_WLH_InviteFriends _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From hiekeen at gmail.com Wed Jun 11 04:48:40 2008 From: hiekeen at gmail.com (Jinyan Huang) Date: Wed, 11 Jun 2008 16:48:40 +0800 Subject: [BiO BB] How to get all TF which target to sox-oct cis-element? Message-ID: How to get all TF which target to sox-oct cis-element ATGCA(T)A(T)A(G/C)A(T)? Thank you very much. -- Best regards, Jinyan Huang (ekeen) School of Life Sciences and Technology, 1302 Room Tongji University Siping Road 1239, Shanghai 200092 P.R. China Tel :0086-21-65981041 Msn: hiekeen at hotmail.com eMail: hiekeen at gmail.com From idoerg at gmail.com Fri Jun 13 02:04:12 2008 From: idoerg at gmail.com (Iddo Friedberg) Date: Thu, 12 Jun 2008 23:04:12 -0700 Subject: [BiO BB] Call for registration: AFP/ Biosapiens 2008 Message-ID: LOCALE: Toronto, Canada (ISMB 2008) DATES: July 18-19, 2008 The Automated Function Prediction (AFP) special interest group and the Biosapiens European network of excellence are teaming up to hold a two-day Special Interest Group (SIG) meeting alongside ISMB 2008. The deluge of genomic information is challenging biologists to annotate this data, from locating genes in the raw data through predicting the function form protein sequence and structure. AFP and Biosapiens share many common goals, and this year we have decided to join forces for a meeting that will deal with a wide scope of gene, protein, and genomic annotations. This meeting is held alongside ISMB, the largest conference on computational biology worldwide. Confirmed keynote speakers include: - Patricia Babbitt, University of California San Francisco, USA - Peer Bork, European Molecular Biology Laboratories, Germany - Andrew Emili, University of Toronto, Canada - Roderic Guig?, Institut Municipal d'Investigaci? M?dica, Universitat Pompeu Fabra, Spain - Barry Honig, Columbia University and Howard Hughes Medical Institute, USA - Kimmen Sj?lander, University of California Berkeley, USA - Olga Troyanskaya, Princeton University, USA Registration: http://www.iscb.org/ismb2008/registration.php (Scroll down to "2-day SIGs". You do not need to register to ISMB to attend the SIGs). FOR MORE INFORMATION: http://2008.BioFunctionPrediction.org/ About ISMB 2008: http://www.iscb.org/ismb2008/ For inquiries, including sponsorship opportunities, please email: afpbiosap2008 at gmail.com -- Iddo Friedberg, Ph.D. CALIT2, mail code 0440 University of California, San Diego 9500 Gilman Drive La Jolla, CA 92093-0440, USA T: +1 (858) 534-0570 T: +1 (858) 646-3100 x3516 http://iddo-friedberg.org From dan.bolser at gmail.com Sat Jun 14 07:38:44 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 14 Jun 2008 13:38:44 +0200 Subject: [BiO BB] what the difference between remediated pdb and pdb? In-Reply-To: <425343C3-DADB-498F-A937-A6CB2C9A6770@embl-hamburg.de> References: <62ed16460806071903i3e1b1c2en57853d611b6ec83@mail.gmail.com> <425343C3-DADB-498F-A937-A6CB2C9A6770@embl-hamburg.de> Message-ID: <2c8757af0806140438j2821f061y46c4ce68bf1f8375@mail.gmail.com> On 09/06/2008, Roberto Mosca wrote: > From the document: > > "3.5 Resolution macromolecular sequence conflicts > Differences in entity sequence assignment between RCSB PDB and MSD-EBI > have > been resolved. Any remaining differences between the chemical sequence > and the > macromolecular sequence have also been resolved." > > I think that this refers only to the DBREF and SEQRES records in the > file. Of > course an alanine cannot become a valine or a tyrosine when going from > the original > to the remediated PDB. I think it can. Lots of 'strange' format inconstancies have been cleaned up, including the unusual practice of labelling amino acids such as tyrosine as alanine if the majority of the side chain is 'unobserved' in the structure. In such cases the tyrosine may look like an alanine (chemically), and was sometimes labelled alanine in the ATOMSEQ. Tons of minor changes were made throughout the PDB files when going from PDB to PDB-REMEDIATED, however, these various changes were not documented... Amazing isn't it? Stupefying? I would be very happy if someone could prove me wrong on this point. It would be possible to get a database of differences by dumping the mmCIF files into XML and then doing an XML diff on all the pairs of files. The PDB's view seems to be 'just start using the remediated files', which you should do if possible. It is also surprising to learn that data in the PDB files such as links to sequence databases are not being kept up to date. For up to date sequence data you need to additionally use the 'sifts' (Structure integration with function, taxonomy and sequence) database: http://www.ebi.ac.uk/msd-srv/docs/sifts/ Hrm... I should add SIFTS to MetaBase ;-) Dan. > > I'm not sure what kind of errors have been fixed but I think there > could have been > inconsistencies between the sequence reported in the SEQRES records > and the > sequence corresponding to the ATOM records in the PDb file itself. > > Roberto > > ............................................ > Dr. Roberto Mosca > > EMBL c/o DESY > Notkestr. 85 > 22607 Hamburg > Germany > > Email: roberto.mosca at embl-hamburg.de > Tel: +49 (0)40 89902 131 > Web: http://www.embl-hamburg.de/~rmosca > ............................................ > > > > On Jun 8, 2008, at 04:03, Xue Li wrote: > >> Hello all, >> >>> From remediated pdb web site http://remediation.wwpdb.org/ >>> index.html, I read >> "Updated references to databases and taxonomies and Resolved >> differences >> between chemical and macromolecular sequences". >> >> Does it mean that for some proteins they will have difference >> sequences in >> remediated pdb and ordinary pdb? >> >> Thanks. >> >> -- >> Xue, Li >> Bioinformatics and Computational Biology program @ ISU >> Ames, IA 50010 >> 515-450-7183 >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- hello From dan.bolser at gmail.com Sat Jun 14 09:42:25 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Sat, 14 Jun 2008 15:42:25 +0200 Subject: [BiO BB] how pdb ID is defined? In-Reply-To: <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> Message-ID: <2c8757af0806140642s459c18dek13343b07302b35cb@mail.gmail.com> On 27/05/2008, Xue Li wrote: > Dear all, > > Maybe this is a naive question. I just noticed that proteins 2GSA and > 4GSA have similar name and denote almost the same protein. > > 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE > (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE > 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE > AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) > > Also, 2ae2 and 1ae1 denote similar proteins. > 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE > 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP > > > Would someone please tell me how PDB ID is defined? Given a list of > pdb ID, can I find biological distance merely based on their pdb IDs? In 'the old days' PDB ID's were chosen by the author, and 'updated' versions of the same protein were indexed by their first digit.. i.e. 1sod / 2sod / etc. for the SuperOxide Dismutase structures. These days the id is arbitrary as you discovered. There is a page dealing with this question on PDBWiki: http://pdbwiki.org/index.php/PDB_code Which is part of the PDB FAQ that is collaboratively maintained there: http://pdbwiki.org/index.php/PDB_FAQ HTH, Dan. > > Thanks a lot. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- hello From sbour at nhlbi.nih.gov Sat Jun 14 09:50:56 2008 From: sbour at nhlbi.nih.gov (Bour, Stephan (NIH/NHLBI) [E]) Date: Sat, 14 Jun 2008 09:50:56 -0400 Subject: [BiO BB] how pdb ID is defined? References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com><62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> <2c8757af0806140642s459c18dek13343b07302b35cb@mail.gmail.com> Message-ID: You may want to check out the DAVID set of tools from the National Institute of Allergy and Infectious Diseases. It was originally designed to address this kind of issue. http://david.abcc.ncifcrf.gov/ Stephan. -----Original Message----- From: Dan Bolser [mailto:dan.bolser at gmail.com] Sent: Sat 6/14/2008 9:42 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] how pdb ID is defined? On 27/05/2008, Xue Li wrote: > Dear all, > > Maybe this is a naive question. I just noticed that proteins 2GSA and > 4GSA have similar name and denote almost the same protein. > > 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE > (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE > 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE > AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) > > Also, 2ae2 and 1ae1 denote similar proteins. > 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE > 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP > > > Would someone please tell me how PDB ID is defined? Given a list of > pdb ID, can I find biological distance merely based on their pdb IDs? In 'the old days' PDB ID's were chosen by the author, and 'updated' versions of the same protein were indexed by their first digit.. i.e. 1sod / 2sod / etc. for the SuperOxide Dismutase structures. These days the id is arbitrary as you discovered. There is a page dealing with this question on PDBWiki: http://pdbwiki.org/index.php/PDB_code Which is part of the PDB FAQ that is collaboratively maintained there: http://pdbwiki.org/index.php/PDB_FAQ HTH, Dan. > > Thanks a lot. > > -- > Xue, Li > Bioinformatics and Computational Biology program @ ISU > Ames, IA 50010 > 515-450-7183 > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- hello _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From dan.bolser at gmail.com Mon Jun 16 02:18:02 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 16 Jun 2008 08:18:02 +0200 Subject: [BiO BB] how pdb ID is defined? In-Reply-To: References: <62ed16460805241813o285a9468u5b5815088f74bbb2@mail.gmail.com> <62ed16460805270805n6ba6b310g3bfba4966b6256e5@mail.gmail.com> <2c8757af0806140642s459c18dek13343b07302b35cb@mail.gmail.com> Message-ID: <2c8757af0806152318j4938b893x6e65f4d0144b55d0@mail.gmail.com> 2008/6/14 Bour, Stephan (NIH/NHLBI) [E] : > You may want to check out the DAVID set of tools from the National Institute of Allergy and Infectious Diseases. It was originally designed to address this kind of issue. > http://david.abcc.ncifcrf.gov/ How do you mean? > Stephan. > > > -----Original Message----- > From: Dan Bolser [mailto:dan.bolser at gmail.com] > Sent: Sat 6/14/2008 9:42 AM > To: General Forum at Bioinformatics.Org > Subject: Re: [BiO BB] how pdb ID is defined? > > On 27/05/2008, Xue Li wrote: >> Dear all, >> >> Maybe this is a naive question. I just noticed that proteins 2GSA and >> 4GSA have similar name and denote almost the same protein. >> >> 4gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE AMINOMUTASE >> (AMINOTRANSFERASE) REDUCED WITH CYANOBOROHYDRATE >> 2gsa: CRYSTAL STRUCTURE OF GLUTAMATE-1-SEMIALDEHYDE >> AMINOMUTASE (AMINOTRANSFERASE, WILD-TYPE FORM) >> >> Also, 2ae2 and 1ae1 denote similar proteins. >> 2ae2: TROPINONE REDUCTASE-II COMPLEXED WITH NADP+ AND PSEUDOTROPINE >> 1ae1: TROPINONE REDUCTASE-I COMPLEX WITH NADP >> >> >> Would someone please tell me how PDB ID is defined? Given a list of >> pdb ID, can I find biological distance merely based on their pdb IDs? > > In 'the old days' PDB ID's were chosen by the author, and 'updated' > versions of the same protein were indexed by their first digit.. i.e. > 1sod / 2sod / etc. for the SuperOxide Dismutase structures. > > These days the id is arbitrary as you discovered. > > There is a page dealing with this question on PDBWiki: > http://pdbwiki.org/index.php/PDB_code > > Which is part of the PDB FAQ that is collaboratively maintained there: > http://pdbwiki.org/index.php/PDB_FAQ > > HTH, > > Dan. > > >> >> Thanks a lot. >> >> -- >> Xue, Li >> Bioinformatics and Computational Biology program @ ISU >> Ames, IA 50010 >> 515-450-7183 >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > > > -- > hello > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- hello From info at bioinformaticsworldwide.com Sun Jun 15 04:35:42 2008 From: info at bioinformaticsworldwide.com (info at bioinformaticsworldwide.com) Date: Sun, 15 Jun 2008 03:35:42 -0500 (CDT) Subject: [BiO BB] Develop WebService Client to Access PDB by Python Message-ID: <2230.82.233.156.213.1213518942.squirrel@www.bioinformaticsworldwide.com> We are happy to start BWW tutorial session this week. You are welcome to share your tutorials with BWW members using your Blogs and/or sending your files to info at bioinformaticsworldwide.com. Today's tutorial is taken from Thuang's Blog. To know more about Thuang's profile please visit http://www.bioinformaticsworldwide.com/profile.php?ID=55 Thuang wrote : " This project is one of my practices: developing a WebService client (normally a web page running on local server) to access public biological database (e.g., PDB). I want to learn and use Python, WebService, CGI, and HTML in this one. I will record each procedure as reference." to read Thang's Tutorial : Develop WebService Client to Access PDB by Python,please click here or copy paste this link in your browser http://www.bioinformaticsworldwide.com/blogs.php?action=show_member_post&ownerID=55&post_id=35 You too you can see your tutorials shared between all BWW members, all you have to do is to write them on your blogs. Sincerely yours, BWW team http://www.bioinformaticsworldwide.com From thlee at bio.mju.ac.kr Tue Jun 17 10:01:06 2008 From: thlee at bio.mju.ac.kr (Tae-Ho Lee) Date: Tue, 17 Jun 2008 23:01:06 +0900 Subject: [BiO BB] Is it possible to parse GenBank flat file by functions in the NCBI toolkit library? Message-ID: I was looking the way parsing GenBank flat file by the NCBI toolkit. However, I was not able to find. Is it possible to parse GenBank flat file by functions in the NCBI toolkit library? Thank you very much. From chirdeeppareek at gmail.com Tue Jun 17 14:27:01 2008 From: chirdeeppareek at gmail.com (chirdeep pareek) Date: Tue, 17 Jun 2008 23:57:01 +0530 Subject: [BiO BB] GenBank flat file parsing Message-ID: <415457350806171127s62184bc7k4354d71a12850d70@mail.gmail.com> hi, myself chirdeep, i have done a great deal of parsing of GenBank file. tell which part u want to parse. From suryabioinfo at yahoo.com Wed Jun 18 04:46:07 2008 From: suryabioinfo at yahoo.com (Surya Gaya) Date: Wed, 18 Jun 2008 01:46:07 -0700 (PDT) Subject: [BiO BB] please help Message-ID: <216141.68576.qm@web59810.mail.ac4.yahoo.com> somebody please tell me the difference between gene expression profile and gene expression fingerprint..how do we usually get or derive each of them..? thanks in advance ? Compose Email: bbb at bioinformatics..org Add to Contacts ? ? Compose Email: bbb at bioinformatics.org Add to Contacts From bsmagic at gmail.com Wed Jun 18 23:04:11 2008 From: bsmagic at gmail.com (Sheng Wang) Date: Thu, 19 Jun 2008 11:04:11 +0800 Subject: [BiO BB] please help In-Reply-To: <216141.68576.qm@web59810.mail.ac4.yahoo.com> References: <216141.68576.qm@web59810.mail.ac4.yahoo.com> Message-ID: <793f8aed0806182004p562430a7q888bee8eba05155e@mail.gmail.com> hi, i guess, gene expression profiling is a kind of *method*, fingerprint is a kind of *result*, the same as 'pattern'. On 6/18/08, Surya Gaya wrote: > > somebody please tell me the difference between gene expression profile and > gene expression fingerprint..how do we usually get or derive each of them..? > > thanks in advance > > > > Compose Email: > bbb at bioinformatics..org > Add to Contacts > > > Compose Email: > bbb at bioinformatics.org > Add to Contacts > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Best Regards Sheng Wang From sankar.achuth at gmail.com Thu Jun 19 09:04:42 2008 From: sankar.achuth at gmail.com (Dr. Achuthsankar S. Nair) Date: Thu, 19 Jun 2008 18:34:42 +0530 Subject: [BiO BB] cophenetic correlation Message-ID: <2b168b460806190604t5714ad6bw1a17cabdf351fd41@mail.gmail.com> A collegaue of mine wants to analyse the cophenetic correlation (the significance between the original similarity/dissimilarity matrix and the dendrogram genetic distance matrix) and also to do the Mantel's Test to correlate the phenograms of different parameters. NTSYSpc, Numerical Taxonomy System, Version 2.2 is a software that does this, but is licenced. Anyone knows a free software alternative ? -- Achuthsankar S Nair www.achu.keralauniversity.edu From marchywka at hotmail.com Thu Jun 19 12:32:12 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Thu, 19 Jun 2008 12:32:12 -0400 Subject: [BiO BB] cophenetic correlation In-Reply-To: <2b168b460806190604t5714ad6bw1a17cabdf351fd41@mail.gmail.com> References: <2b168b460806190604t5714ad6bw1a17cabdf351fd41@mail.gmail.com> Message-ID: With regards to this request specifically and in general, if you could post a link to a paper or web page that describes the underlying algorithm, you might reach a wider audience ( who may not know they have a solution ). As far as that goes, I often "re-invent the wheel" and you may find someone who has something close he could adapt ( obvious caveats would apply but if you are really stuck for something free that may be a good collaboration op). Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 404-788-1216 (C)<- leave message 989-348-4796 (P)<- emergency only marchywka at hotmail.com Note: If I am asking for free stuff, I normally use for hobby/non-profit information but may use in investment forums, public and private. Please indicate any concerns if applicable. Note: Hotmail is possibly blocking my mom's entire ISP - try me on marchywka at yahoo.com if no reply here. Thanks. > Date: Thu, 19 Jun 2008 18:34:42 +0530 > From: sankar.achuth at gmail.com > To: bbb at bioinformatics.org > CC: shaijukvm at yahoo.co.in > Subject: [BiO BB] cophenetic correlation > > A collegaue of mine wants to analyse the cophenetic correlation (the > significance between the original similarity/dissimilarity matrix and the > dendrogram genetic distance matrix) and also to do the Mantel's Test to > correlate the phenograms of different parameters. NTSYSpc, Numerical > Taxonomy System, Version 2.2 is a software that does this, but is licenced. > Anyone knows a free software alternative ? > > -- > Achuthsankar S Nair > www.achu.keralauniversity.edu > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ The i?m Talkathon starts 6/24/08.? For now, give amongst yourselves. http://www.imtalkathon.com?source=TXT_EML_WLH_LearnMore_GiveAmongst From pete at softgenetics.com Thu Jun 19 15:22:04 2008 From: pete at softgenetics.com (Pete Marchetto) Date: Thu, 19 Jun 2008 15:22:04 -0400 Subject: [BiO BB] please help In-Reply-To: References: <216141.68576.qm@web59810.mail.ac4.yahoo.com> Message-ID: <6544FA90-4735-4EA3-967B-4D559166F734@softgenetics.com> After consulting with one of our staff biologists, and surveying some articles, it seems like this is the case: Gene Expression Profile: This is the difference either between two organisms' genomes, or between an organism and the averaged experimental norm. In other words, it is the entire definition for an individual. Gene Expression Fingerprint: This is a subset of the profile that accounts for a particular trait, such as markers for a disease. On average, the profile would be in the thousands of genes, while the fingerprint would be in the dozens to hundreds. Anyone else got a better description? -Peter Marchetto On Jun 18, 2008, at 7:31 PM, Pete Marchetto wrote: > > > Begin forwarded message: > >> From: Surya Gaya >> Date: June 18, 2008 4:46:07 AM EDT >> To: bbb at bioinformatics.org >> Subject: [BiO BB] please help >> Reply-To: "General Forum at Bioinformatics.Org" > > >> >> somebody please tell me the difference between gene expression >> profile and gene expression fingerprint..how do we usually get or >> derive each of them..? >> >> thanks in advance >> >> >> >> Compose Email: >> bbb at bioinformatics..org >> Add to Contacts >> >> >> Compose Email: >> bbb at bioinformatics.org >> Add to Contacts >> >> >> >> _______________________________________________ >> BBB mailing list >> BBB at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bbb >> > From jyotirusia at gmail.com Wed Jun 25 06:46:01 2008 From: jyotirusia at gmail.com (jyoti rusia) Date: Wed, 25 Jun 2008 16:16:01 +0530 Subject: [BiO BB] software for protein threading In-Reply-To: <1213033401.484d6bb98959d@webmail.upv.es> References: <1213033401.484d6bb98959d@webmail.upv.es> Message-ID: <1a423b840806250346k9f5b7dfw775713f2495ae9b4@mail.gmail.com> hiii can anyone tell me any tool name and link for finding, SNP in given sequences apart from SNP FINDER tool. thanks On 6/9/08, Javier Forment Millet wrote: > > Hi, all... > > We are attempting to do a temptative functional annotation for EST-derived > partial ORFs which didn't found an annotated similar sequence in BLAST > searches. Could anyone suggest a software for automated fold recognition by > threading in local computers? > > Thanks in advance, > > Javier. > > > -- > Javier Forment Millet > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > jforment at ibmcp.upv.es > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Jyoti Rusia The difference between a successful person and others is not a lack of strength, not a lack of knowledge, but rather a lack in will.....Vince Lombardi From dan.bolser at gmail.com Wed Jun 25 16:05:32 2008 From: dan.bolser at gmail.com (Dan Bolser) Date: Wed, 25 Jun 2008 22:05:32 +0200 Subject: [BiO BB] software for protein threading In-Reply-To: <1213033401.484d6bb98959d@webmail.upv.es> References: <1213033401.484d6bb98959d@webmail.upv.es> Message-ID: <2c8757af0806251305y53181612t9081b619bccefc0@mail.gmail.com> 2008/6/9 Javier Forment Millet : > Hi, all... > > We are attempting to do a temptative functional annotation for EST-derived > partial ORFs which didn't found an annotated similar sequence in BLAST > searches. Could anyone suggest a software for automated fold recognition by > threading in local computers? Hi Javier, Not sure if this is really helpful or not, but I have been working on a project called PDBWiki, which maintains an FAQ about protein structures. Although we haven't covered threading explicitly in the FAQ, perhaps the answer to the following question is useful for you: How do I build a homology model? http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_build_a_homology_model.3F This would probably be your next step after running a threading algorithm to obtain a sequence / structure alignment. However, as Martin pointed out, the first thing to try is probably psi-blast, or a search against a library of HMMs. This is because sometimes you can find very reliable alignments between sequences that have very low sequence identity (and so fail to 'blast'). Cheers, Dan. > Thanks in advance, > > Javier. > > > -- > Javier Forment Millet > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > Tlf.:+34-96-3877858 > FAX: +34-96-3877859 > jforment at ibmcp.upv.es > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- PDBWiki - http://PDBWiki.Org From jforment at ibmcp.upv.es Thu Jun 26 06:13:23 2008 From: jforment at ibmcp.upv.es (Javier Forment Millet) Date: Thu, 26 Jun 2008 12:13:23 +0200 Subject: [BiO BB] software for protein threading In-Reply-To: <2c8757af0806251305y53181612t9081b619bccefc0@mail.gmail.com> References: <1213033401.484d6bb98959d@webmail.upv.es> <2c8757af0806251305y53181612t9081b619bccefc0@mail.gmail.com> Message-ID: <1214475203.48636bc3b9b8a@webmail.upv.es> Hi,... I've run iprscan and, of course, it allows functional annotation for some orphan proteins. Now, the next step is trying to do threading with the rest of orphan sequences. I'm not interested in building an structure model for these proteins. I just want to be able to identify a putative CATH/SCOP folding for them, so that we can do a temptative functional annotation based on the predicted/confirmed function for that folding. I've found programs such as threader, prospect, frost, analyst, raptor, tasser, forte, modeller, SP4, etc. But I have no experience with them (and even don't know if some of them could be useful for what we want), so I would like to get feedback from people having used them... Cheers, Javier. > 2008/6/9 Javier Forment Millet : > > Hi, all... > > > > We are attempting to do a temptative functional annotation for EST-derived > > partial ORFs which didn't found an annotated similar sequence in BLAST > > searches. Could anyone suggest a software for automated fold recognition by > > threading in local computers? > > Hi Javier, > > Not sure if this is really helpful or not, but I have been working on > a project called PDBWiki, which maintains an FAQ about protein > structures. Although we haven't covered threading explicitly in the > FAQ, perhaps the answer to the following question is useful for you: > > How do I build a homology model? > > http://pdbwiki.org/index.php/PDB_FAQ#Q:_How_do_I_build_a_homology_model.3F > > > This would probably be your next step after running a threading > algorithm to obtain a sequence / structure alignment. However, as > Martin pointed out, the first thing to try is probably psi-blast, or a > search against a library of HMMs. This is because sometimes you can > find very reliable alignments between sequences that have very low > sequence identity (and so fail to 'blast'). > > > Cheers, > Dan. > > > > Thanks in advance, > > > > Javier. > > > > > > -- > > Javier Forment Millet > > Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV > > Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta > E > > Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain > > Tlf.:+34-96-3877858 > > FAX: +34-96-3877859 > > jforment at ibmcp.upv.es > > > > > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > -- > PDBWiki - http://PDBWiki.Org > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Javier Forment Millet Instituto de Biolog?a Celular y Molecular de Plantas (IBMCP) CSIC-UPV Ciudad Polit?cnica de la Innovaci?n (CPI) Edificio 8 E, Escalera 7 Puerta E Calle Ing. Fausto Elio s/n. 46022 Valencia, Spain Tlf.:+34-96-3877858 FAX: +34-96-3877859 jforment at ibmcp.upv.es From barry.hardy at vtxmail.ch Thu Jun 26 07:25:15 2008 From: barry.hardy at vtxmail.ch (Barry Hardy) Date: Thu, 26 Jun 2008 13:25:15 +0200 Subject: [BiO BB] Drug Discovery Informatics, eCheminfo Autumn Meeting Message-ID: <48637C9B.5090008@vtxmail.ch> Latest Advances in Drug Discovery Informatics eCheminfo Autumn Community of Practice Meeting 14-17 October 2008 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link: Website: http://echeminfo.com/COMTY_conferences Blog: http://barryhardy.blogs.com/cheminfostream/ Program (pdf): http://barryhardy.blogs.com/cheminfostream/files/eChemProgramBrynMawr08-Final-v2.pdf Themes: Cheminformatics, Bioinformatics, Medicinal Chemistry, Drug Discovery Innovation, Structure-based Drug Design, Screening, Docking, Structural Biology, Predictive Toxicology, Predictive ADME, Chemogenomics Program Summary Docking & Scoring, chaired by Chaya Duraiswami (GlaxoSmithKline) Application of MM-PBSA Free Energy Methods in Drug Discovery, chaired by Judith Lalonde (Bryn Mawr College) Accurate Calculation of pKas, chaired by Paul Labute (Chemical Computing Group) In Silico-based Chemogenomics, chaired by Fabrice Moriaud (MEDIT) PDB Ligands: Analysing their Structure & Binding Data, chaired by Marc Nicklaus (National Institutes of Health) Predictive ADME, chaired by Anthony E. Klon (Pharmacopeia Drug Discovery) Predictive Toxicology, chaired by Artem Cherkasov (University of British Columbia) Pre-Conference Workshop, 13 October Best Practices Virtual Screening Workshop chaired by Barry Hardy (Douglas Connect) Speakers John Irwin (UCSF), Georgia McGaughey (Merck), Johannes H. Voigt (Schering Plough), Lance Westerhoff (Quantum Bio), Zsolt Zsoldos (SimBioSys), Alexey Ornufriev (Virginia Tech), David Case (Rutgers University), Rommie Amaro (USCD), Peter Coveney (Univ. College London), Anna Kohlmann (Ariad Pharmaceuticals), Scott Brown (Abbott), Emil Alexov (Clemson University), Jens Erik Nielsen (University College Dublin, Ireland), Matthew Davies (Jenner Institute, UK), Maja Mihajlovic (City College of New York), Michael Keiser (UCSF), Brian Marsden (University of Oxford, UK), Alex Tropsha (UNC), John Westbrook (Rutgers), Howard J Feldman (CCG), Igor V. Filippov (NCI), Raul Cachau (ATP, SAIC-Frederick), Vincent T. Moy (University of Miami), Paul Hawkins (OpenEye), Yulia Borodina (NCBI), Gerhard Wolber (Inte:Ligand, Austria), Marc Nicklaus (NCI), James P. Snyder (Emory), Anne Chaka (NIST), Esther Kellenberger (Univ. Strasbourg, France), Renxiao Wang (SIOC, Shanghai, PR China), Jim Dunbar (University of Michigan), Janna Wehrle (NIGMS), Anton Hopfinger (University of New Mexico), Heidi Einolf (Novartis), Yojiro Sakiyama (Pfizer), Olga Obrezanova (BioFocus DPI, UK), Anthony E. Klon (Pharmacopeia), Artem Cherkasov (University of British Columbia, Canada), Ann Richards (US EPA), Curt Breneman (RPI), Barry Hardy (Douglas Connect), Weida Tong (FDA) CFP We invite contributed talks from members of academic, government research and commercial organizations on areas of new research and innovation involving drug discovery research informatics. The work presented should involve innovative new method development or application to drug discovery problems and involving methods from computational chemistry, computational biology, cheminformatics or bioinformatics. Studies including experimental work in medicinal chemistry, screening, experimental toxicology, pre-clinical evaluation, lead optimisation and translational medicine are welcome. Abstracts (300-500 words) should be submitted to echeminfo -[at]- douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008. Bursary Award Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants can be working in any area of research related to drug discovery at the postdoctoral, graduate student and senior undergraduate levels. To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations related to drug discovery (300-500 words) to echeminfo -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008. Poster Session All InterAction Meeting registrants are eligible to present a Conference Poster. The Poster Sessions will take place in the evenings in Thomas Great Hall on campus, where refreshments and dinner are also served. Poster Abstracts (300-500 words) with Title, Institution, Authors and Contact Information should be submitted to barry.hardy -[at]- douglasconnect.com Abstracts will be considered based on date of submission and quality, and will be reviewed and accepted as they are received. To be considered for the formal program, they should be submitted at the very latest by 31 August 2008. We gratefully acknowledge the sponsorship support of: Chemical Computing Group Merck Research Laboratories SimBioSys Contact: Program: Dr. Barry Hardy, eCheminfo Community of Practice, Douglas Connect. Tel: +41 61 851 0170. barry.hardy -[at]- douglasconnect.com Registration Enquiries: Nicki Douglas, Douglas Connect, Baermeggenweg 14, 4314 Zeiningen, Switzerland. Tel: +41 61 851 0461. echeminfo -[at]- douglasconnect.com or go to: http://echeminfoBM810.eventsbot.com From jeff at bioinformatics.org Thu Jun 26 16:19:46 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Thu, 26 Jun 2008 16:19:46 -0400 Subject: [BiO BB] Bioinformatics.Org courses for July Message-ID: <4863F9E2.50503@bioinformatics.org> Bioinformatics.Org is offering the following courses next month. ------------------------------------------------------------------------------ BI211A Protein-Protein Interactions; Jul 7-11, 2008 ------------------------------------------------------------------------------ With systems biology budding as a discipline, there is a colossal need for biologists to understand the interactions within biological networks. There has been much talk about systems biology and protein-protein interactions (PPI), and this course will dig into some of the fundamental issues concerning PPIs, their need and usage. The exercises and take-home messages in this course will encourage students to give some thought to the topics covered and hopefully build some excitement about the field of systems biology. http://wiki.bioinformatics.org/BI211A_Protein-Protein_Interactions ------------------------------------------------------------------------------ CS101E Python for Biologists, Level 1; Jul 7-11, 2008 ------------------------------------------------------------------------------ This course aims at teaching Biologists how to use Python as a programming language to automate routine data management tasks in biological research and solve difficult data-related computational problems. Data could be DNA or amino acid sequence, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. http://wiki.bioinformatics.org/CS101E_Python_for_Biologists,_Level_1 ------------------------------------------------------------------------------ CS101C MySQL for Biologists, Level 1; Jul 14-18, 2008 ------------------------------------------------------------------------------ Taught in the context of biological research, this course helps biologists learn how to use the database management system, MySQL to store, manage and query biological information. http://wiki.bioinformatics.org/CS101C_MySQL_for_Biologists,_Level_1 ------------------------------------------------------------------------------ CS102E Python for Biologists, Level 2; Jul 21-25, 2008 ------------------------------------------------------------------------------ This course aims at teaching Biologists how to use Python as a programming language to automate routine data management tasks in biological research and solve difficult data-related computational problems. Data could be DNA or Amino acid sequence, microarray data, images, mass spectrometry data, LIMS data, or any other kind of biological information. http://wiki.bioinformatics.org/CS102E_Python_for_Biologists,_Level_2 ------------------------------------------------------------------------------ CS102C MySQL for Biologists, Level 2; Jul 28-Aug 1, 2008 ------------------------------------------------------------------------------ Taught in the context of biological research, this course shows biologists how to use the database management system MySQL to store and retrieve data. It is a continuation of CS101C MySQL for Biologists, Level 1 and covers advanced topics and projects. http://wiki.bioinformatics.org/CS102C_MySQL_for_Biologists,_Level_2 Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From kiran.soorya at gmail.com Mon Jun 30 11:41:05 2008 From: kiran.soorya at gmail.com (soorya kiran) Date: Mon, 30 Jun 2008 21:11:05 +0530 Subject: [BiO BB] algorithm for codon optimization In-Reply-To: References: Message-ID: Can any one help me to find a publication which describes the implementation of Monte Carlo algorithm in Codon optimization of prokaryote ? advance thanks Srijith Confidentiality Statement :- The contents of this e-mail, including its attachment, are intended for the exclusive use of the recipient and may contain confidential or privileged information. If you are not the intended recipient, you are strictly prohibited from reading, using, disclosing, copying, or distributing this e-mail or any of its contents. If you received this e-mail in error, please notify the sender by reply e-mail immediately and permanently delete this e-mail and its attachments, along with any copies thereof. Thank you. -- SooryaKiran Bioinformatics (P) LTD, Industry Incubation Centre, University of Kerala, Karyavattom Campus, Thiruvananthapuram, Keralam, India. 695 581 Ph : +91 471 2414593 Corporate Office: T-TBI, Nila,Technopark, Thiruvanathapuram, 695 581 Keralam, India Ph - +91 471 4060948 www.sooryakiran.com Email : kiran.soorya at gmail.com Confidentiality Statement :- The contents of this e-mail, including its attachment, are intended for the exclusive use of the recipient and may contain confidential or privileged information. If you are not the intended recipient, you are strictly prohibited from reading, using, disclosing, copying, or distributing this e-mail or any of its contents. If you received this e-mail in error, please notify the sender by reply e-mail immediately and permanently delete this e-mail and its attachments, along with any copies thereof. Thank you. From maheshchandran09 at gmail.com Mon Jun 30 23:07:54 2008 From: maheshchandran09 at gmail.com (mahesh chandran) Date: Tue, 1 Jul 2008 08:37:54 +0530 Subject: [BiO BB] Highly represntative Folds Message-ID: Hi friends ,just help me out with this problem.How to find the highly representative protein folds ?In other words, i would like to know the top 10 folds that are most commonly seen in proteins.