From ashwathy.bl at gmail.com Tue Jul 1 00:22:57 2008 From: ashwathy.bl at gmail.com (Ashwathy) Date: Tue, 1 Jul 2008 09:52:57 +0530 Subject: [BiO BB] implementation of Monte Carlo algorithm in Codon optimization of prokaryote In-Reply-To: <215bd4440806302121u4e3930b1ydededdaf8f389b25@mail.gmail.com> References: <215bd4440806302120i2cc55591yafc28a444494cf19@mail.gmail.com> <215bd4440806302121u4e3930b1ydededdaf8f389b25@mail.gmail.com> Message-ID: <215bd4440806302122s192fbcb9wb4dcccc969795e0c@mail.gmail.com> Can any one help me to find a publication which describes the implementation of Monte Carlo algorithm in Codon optimization of prokaryote ? Rgds aswathi From marchywka at hotmail.com Tue Jul 1 14:13:54 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 1 Jul 2008 14:13:54 -0400 Subject: [BiO BB] implementation of Monte Carlo algorithm in Codon optimization of prokaryote In-Reply-To: <215bd4440806302122s192fbcb9wb4dcccc969795e0c@mail.gmail.com> References: <215bd4440806302120i2cc55591yafc28a444494cf19@mail.gmail.com> <215bd4440806302121u4e3930b1ydededdaf8f389b25@mail.gmail.com> <215bd4440806302122s192fbcb9wb4dcccc969795e0c@mail.gmail.com> Message-ID: > Date: Tue, 1 Jul 2008 09:52:57 +0530 > From: ashwathy.bl at gmail.com > To: bbb at bioinformatics.org > Subject: [BiO BB] implementation of Monte Carlo algorithm in Codon optimization of prokaryote > > Can any one help me to find a publication which describes the implementation > of Monte Carlo algorithm in Codon optimization of prokaryote ? > you can usually contact authors directly if you can find a related work as they may know how to contact other authors you can't find easily, http://www.scirus.com/srsapp/search?q=%22codon+optimization%22+%22monte+carlo%22&t=all&sort=0&g=s http://www.google.com/search?hl=en&q=site%3Aciteseer.ist.psu.edu+%22codon+optimization%22 also try pubmed. First hit on scirus is this, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933141 Only a few US patents mention both terms and none appear to be relevant. > Rgds > aswathi > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb _________________________________________________________________ Enter the Zune-A-Day Giveaway for your chance to win ? day after day after day http://www.windowslive-hotmail.com/ZuneADay/?locale=en-US&ocid=TXT_TAGLM_Mobile_Zune_V1 From joshuabhk at gmail.com Tue Jul 1 14:32:02 2008 From: joshuabhk at gmail.com (Bong-Hyun Kim) Date: Tue, 1 Jul 2008 13:32:02 -0500 Subject: [BiO BB] implementation of Monte Carlo algorithm in Codon optimization of prokaryote In-Reply-To: References: <215bd4440806302120i2cc55591yafc28a444494cf19@mail.gmail.com> <215bd4440806302121u4e3930b1ydededdaf8f389b25@mail.gmail.com> <215bd4440806302122s192fbcb9wb4dcccc969795e0c@mail.gmail.com> Message-ID: <4cd067f00807011132x1a1c893bue91c473eacb82564@mail.gmail.com> It seems to me that googling with "codon" and "simulation" seems to give me a lot of pretty interesting hits. http://www.google.com/search?hl=en&q=codon+simulation&btnG=Search Bong-Hyun Kim Biophysics Program Department of Biochemistry UT Southwestern Medical Center at Dallas On Tue, Jul 1, 2008 at 1:13 PM, Mike Marchywka wrote: > > > > > Date: Tue, 1 Jul 2008 09:52:57 +0530 > > From: ashwathy.bl at gmail.com > > To: bbb at bioinformatics.org > > Subject: [BiO BB] implementation of Monte Carlo algorithm in Codon > optimization of prokaryote > > > > Can any one help me to find a publication which describes the > implementation > > of Monte Carlo algorithm in Codon optimization of prokaryote ? > > > > you can usually contact authors directly if you can find a related work as > they may know > how to contact other authors you can't find easily, > > > http://www.scirus.com/srsapp/search?q=%22codon+optimization%22+%22monte+carlo%22&t=all&sort=0&g=s > > > http://www.google.com/search?hl=en&q=site%3Aciteseer.ist.psu.edu+%22codon+optimization%22 > > also try pubmed. > First hit on scirus is this, > > http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933141 > > Only a few US patents mention both terms and none appear to be relevant. > > > > > Rgds > > aswathi > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > _________________________________________________________________ > Enter the Zune-A-Day Giveaway for your chance to win ? day after day after > day > > http://www.windowslive-hotmail.com/ZuneADay/?locale=en-US&ocid=TXT_TAGLM_Mobile_Zune_V1 > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From boris.steipe at utoronto.ca Tue Jul 1 19:11:33 2008 From: boris.steipe at utoronto.ca (Boris Steipe) Date: Tue, 1 Jul 2008 19:11:33 -0400 Subject: [BiO BB] Highly represntative Folds In-Reply-To: References: Message-ID: Thats a bit of an ill-posed question. Most commonly seen among all genes? Among all solved protein structures? Superfamilies with the largest number of family members? Most frequent if you would take a random sample of proteins from a living cell? ... There are many possible sets to choose from, not all of them in some way biologically relevant. If you want an overview of what's out there, browse CATH or SCOP. CATH architectures and SCOP superfamilies probably come closest to a concept of "representative". http://www.cathdb.info/ http://scop.mrc-lmb.cam.ac.uk/scop/ HTH, Boris On 30-Jun-08, at 11:07 PM, mahesh chandran wrote: > 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. > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From ashwathy.bl at gmail.com Tue Jul 1 23:50:03 2008 From: ashwathy.bl at gmail.com (Ashwathy) Date: Wed, 2 Jul 2008 09:20:03 +0530 Subject: [BiO BB] algorithm for codon optimization In-Reply-To: References: Message-ID: <215bd4440807012050m6d94c370s7d7c2302bbd9fc54@mail.gmail.com> hi srijith.. here r some links..pls go through these .. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933141 http://www.biomedcentral.com/1471-2105/7/285/table/T1 http://www.biomedcentral.com/1471-2105/7/285 http://www.scirus.com/srsapp/search?q=%22codon+optimization%22+%22monte+carlo%22&t=all&sort=0&g=s http://www.google.com/search?hl=en&q=site%3Aciteseer.ist.psu.edu+%22codon+optimization%22 First hit on scirus is this, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1933141 http://www.google.com/search?hl=en&q=codon+simulation&btnG=Search On Mon, Jun 30, 2008 at 9:11 PM, soorya kiran wrote: > 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. > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From jeff at bioinformatics.org Mon Jul 7 13:37:17 2008 From: jeff at bioinformatics.org (J.W. Bizzaro) Date: Mon, 07 Jul 2008 13:37:17 -0400 Subject: [BiO BB] Bioinformatics Career Survey Message-ID: <4872544D.6080309@bioinformatics.org> Via BioinformaticsZen.com: ``When I wrote a post about my opinion of doing a career in bioinformatics I got the impression from the comments that this was something many people wanted more information about. Pedro and I had some discussion, and thought it might be interesting to create an online survey, to get current researchers? opinions of working in the field of bioinformatics. So, the below survey begins today (July 1) and is filled out by as many people as possible over the course the next month. The data is then released into the public domain at the start of next month (August 1). Anyone who is then interested can contribute back analysis of this data, so that on September 1 hopefully we can compile together lots of interesting statistics and graphs into a handy document discussing the highs and lows of career in bioinformatics.'' The survey can be found at the Bioinformatics.Org Career Center through July: http://www.bioinformatics.org/jobs/ BioinformaticsZen.com article: http://www.bioinformaticszen.com/2008/07/creating-a-picture-of-different-careers-in-bioinformatics/ Cheers, Jeff -- J.W. Bizzaro Bioinformatics Organization, Inc. (Bioinformatics.Org) E-mail: jeff at bioinformatics.org Phone: +1 978 562 4800 -- From anubhav_rast at yahoo.co.in Tue Jul 8 00:16:58 2008 From: anubhav_rast at yahoo.co.in (anubhav rastogi) Date: Tue, 8 Jul 2008 09:46:58 +0530 (IST) Subject: [BiO BB] Rules for codon optimization Message-ID: <988740.91227.qm@web8613.mail.in.yahoo.com> Hello all, I am working on a project on Codon optimization. I want to know the rules involved for codon optimization for prokaryotes and eukaryotes,like GC content, AT preference, hydrophobicities. can u please list me the papers or people who are working at this end Anubhav Bring your gang together. Do your thing. Find your favourite Yahoo! group at http://in.promos.yahoo.com/groups/ From kanagasa at i2r.a-star.edu.sg Wed Jul 9 22:57:16 2008 From: kanagasa at i2r.a-star.edu.sg (Kanagasabai Rajaraman) Date: Thu, 10 Jul 2008 10:57:16 +0800 Subject: [BiO BB] 2nd CFP: Bioinformatics Track @ ACM Symposium on Applied Computing (SAC) 2009 - due Aug 16, 2008 Message-ID: <162B8AFBFBBB2148A9A1B8F9C575342801FDF414@mailbe01.teak.local.net> * Apologies if you receive multiple copies of this announcement * SAC 2009 The 24th ACM Symposium on Applied Computing March 8 - 12, 2009, Waikiki Beach, Honolulu, Hawaii, USA Bioinformatics Track CALL FOR PAPERS SAC 2009 The ACM Symposium on Applied Computing (SAC) is a primary forum for applied computer scientists and application developers from around the world to interact and present their work. SAC 2009 is sponsored by the ACM Special Interest Group on Applied Computing (SIGAPP) and is presented in cooperation with other ACM Special Interest Groups. For more information on ACM SAC 2009, please visit: http://www.acm.org/conferences/sac/sac2009/ Bioinformatics Track A large part of the information to support biological and biomedical research is available in an increasingly wide variety of rapidly-growing decentralized databases. The challenge is to obtain information and knowledge from these databases using innovative computational approaches to support and promote biological and biomedical research. One example of such a computational challenge is in identifying biological pathways using data, information, and knowledge scattered over heterogeneous databases. Computational tools using system-theoretic approaches are needed to model metabolic pathways, signal-transduction pathways, genetic regulatory circuits and biological systems. By comparing the genomes and pathways of several species at a high level, we hope to understand how stable biological systems have evolved. Over the last few years, microarray data have provided many insights into the transcriptome and into cellular functions. These data are now increasingly complemented by mass spectrometry data of the proteome, whose analysis poses new computational challenges. Track Topics: * Algebraic Biology * Bioinformatics for diseases * Computational genomics and systems biology * Data visualization and visual analytics * Databases & Data Integration * DNA assembly, clustering and mapping * Errors and inconsistencies in biological databases * Gene Expression/regulation & Microarrays * Genomes and protein analysis * High-performance bio-computing * Integrative approaches for drug design * Integrative data and text mining approaches * Life sciences databases and ontologies * Machine learning, data integration and data mining in the life sciences * Molecular sequence analysis, modeling and simulation * Parallel architectures and algorithms for biological applications * Pathways, Networks, Systems Biology * Prediction and integration of metabolic and regulatory networks * Protein & RNA Structure and Function * Protein-protein Interactions, prediction, and Molecular Networks * Query processing and optimization for biological data * Semantic web for the life sciences * Sequence Analysis & Alignment, Assembly * SNPs and Haplotyping * Structural and functional bioinformatics * System Biology and Modeling * Virtual cell modeling Important Dates Abstracts/Paper Due: August 16, 2008 (Firm) Author notification: October 11, 2008 Camera-Ready Due: October 25, 2008 Paper Registration and Submission Guidelines Authors must register their intent to submit a paper using the conference management system, eCMS, at: http://sac.cs.iupui.edu/SAC2009/ and obtain a Paper Identification Number. Authors must use eCMS and the Paper Id for further paper submission and other correspondence. All papers should represent original and previously unpublished works that are currently not under review in any conference or journal. Both basic and applied research papers are welcome. The initial paper submission should not be more than 15 pages long using 11-point font and 1 inch margins on all four sides on letter size paper. The author(s) name(s) and address(s) must NOT appear in the body of the submitted paper, and self-references should be in the third person. This is to facilitate blind review required by ACM. All submitted papers must include the paper identification number on the front page, above the title of the paper provided to you by the eCMS when you register your paper. All enquiries and questions should be directed to the Track Chairs. Additional details are available at the track home page at http://www.cs.iupui.edu/~bioin and at the conference home page at http://www.acm.org/conferences/sac/sac2009. Conference Paper Publication All papers will be fully refereed and undergo a blind review process by at least three referees. The conference proceedings will be published by ACM. Hence, all accepted papers should be submitted in ACM 2-column camera-ready format for publication in the symposium proceedings. The final version of the paper should not be more than 5 pages long. An additional 3 pages are allowed with a charge of 80USD per extra page. Final Camera-ready submissions must follow the template available at: http://www.acm.org/conferences/sac/sac2009/downloads09.htm Journal Paper Publication Expanded version of 4-5 top ranking papers will be accepted for publication in the International Journal of Data Mining and Bioinformatics (ijdmb at inderscience.com). Authors will be contacted after the presentation of these papers at the SAC Conference in Hawaii. Poster Publication of Selected Papers A set of selected papers will be accepted as poster papers by invitation only and will be published as short papers in the symposium proceedings. Track Chairs Mathew J. Palakal Indiana University Purdue University Indianapolis, USA Email: mpalakal at iupui.edu Rajaraman Kanagasabai Institute for Infocomm Research, Singapore Email: kanagasa at i2r.a-star.edu.sg ********************** ANNOUNCEMENT ******************************** We are moving to Fusionopolis! With effect of Monday, 28 July 2008, our official address will be: Institute for Infocomm Research, 1 Fusionopolis Way, #21-01 Connexis, Singapore 138632. Main line: +65 64082000. Please visit http://www.fusionopolis.a-star.edu.sg/ for more information on Fusionopolis. ******************************************************************* ------------ Institute For Infocomm Research - Disclaimer -------------This email is confidential and may be privileged. If you are not the intended recipient, please delete it and notify us immediately. Please do not copy or use it for any purpose, or disclose its contents to any other person. Thank you -------------------------------------------------------- From me.lixue at gmail.com Mon Jul 14 18:57:44 2008 From: me.lixue at gmail.com (Xue Li) Date: Mon, 14 Jul 2008 17:57:44 -0500 Subject: [BiO BB] how to calculate the atom distance between antigen and antibody Message-ID: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> hello all, I am new in this. If I have 1JPS.pdb, would someone please tell me how to calculate the atom distance between antigen and antibody? Thank you. Li From phoebe.chen at deakin.edu.au Tue Jul 15 01:18:34 2008 From: phoebe.chen at deakin.edu.au (Phoebe Chen) Date: Tue, 15 Jul 2008 15:18:34 +1000 Subject: [BiO BB] APBC2009 Deadline Approaching Message-ID: <20080715151834.wmxujcy4qos88kko@www.deakin.edu.au> ************************************************************************** APBC2009 Deadline Approaching - Full Paper Submission on 20 July (5 days) this SUNDAY **************************************************************************** ============================================= CALL FOR PAPERS - APBC2009 The Seventh Asia-Pacific Bioinformatics Conference (APBC2009) Beijing, China, 13-16 January 2009 http://bioinfo.au.tsinghua.edu.cn/apbc2009/ ============================================== The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The Seventh Asia-Pacific Bioinformatics Conference, APBC2009 will be held in Beijing, China, following the 2008 Olympic Games. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. --------------------------------------------------------------- Important Dates Paper submission deadline July 20, 2008 Paper acceptance decision Sep 10, 2008 Camera-ready copy of papers and Author registration Oct 10, 2008 Poster submission open July 20, 2008 Poster submission deadline Sept 20, 2008 Poster acceptance decision Oct 1, 2008 Registration open Sept 20, 2008 Early-bird registration Nov 20, 2008 Conference Jan 13-16, 2009 From phoebe at deakin.edu.au Tue Jul 15 01:32:17 2008 From: phoebe at deakin.edu.au (Phoebe Chen) Date: Tue, 15 Jul 2008 15:32:17 +1000 Subject: [BiO BB] APBC2009 Deadline Approaching Message-ID: <20080715153217.1g2g2b8dw8cco0oo@www.deakin.edu.au> **************************************************************************** APBC2009 Deadline Approaching - Full Paper Submission on 20 July (5 days) this SUNDAY **************************************************************************** ============================================= CALL FOR PAPERS - APBC2009 The Seventh Asia-Pacific Bioinformatics Conference (APBC2009) Beijing, China, 13-16 January 2009 http://bioinfo.au.tsinghua.edu.cn/apbc2009/ ============================================== The Asia Pacific Bioinformatics Conference (APBC) series, founded in 2003, is an annual international forum for exploring research, development and applications of Bioinformatics and Computational Biology. The Seventh Asia-Pacific Bioinformatics Conference, APBC2009 will be held in Beijing, China, following the 2008 Olympic Games. The aim of the conference is to bring together researchers, professionals, and industrial practitioners from all over the world for interaction and exchange of knowledge and ideas in all areas of bioinformatics and computational biology. --------------------------------------------------------------- Important Dates Paper submission deadline July 20, 2008 *** Paper acceptance decision Sep 10, 2008 Camera-ready copy of papers and Author registration Oct 10, 2008 Poster submission open July 20, 2008 Poster submission deadline Sept 20, 2008 Poster acceptance decision Oct 1, 2008 Registration open Sept 20, 2008 Early-bird registration Nov 20, 2008 Conference Jan 13-16, 2009 From floris at crs4.it Tue Jul 15 10:33:26 2008 From: floris at crs4.it (Matteo Floris) Date: Tue, 15 Jul 2008 16:33:26 +0200 Subject: [BiO BB] how to calculate the atom distance between antigen and antibody In-Reply-To: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> References: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> Message-ID: <0D9D8372-11E1-48A9-AFF2-F6E171C3010D@crs4.it> Hi Li, you can do it with PyMol. M. Matteo Floris CRS4 Bioinformatica http://www.bioinformatica.crs4.org phone: +39 070 9250 422 fax: +39 070 92433114 ________________________________ > hello all, > > I am new in this. > > If I have 1JPS.pdb, would someone please tell me how to calculate > the atom > distance between antigen and antibody? > > Thank you. > > Li > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From pfern at igc.gulbenkian.pt Tue Jul 15 11:37:03 2008 From: pfern at igc.gulbenkian.pt (Pedro Fernandes) Date: Tue, 15 Jul 2008 16:37:03 +0100 Subject: [BiO BB] Search and Mining, Bioinformatics Training Course Message-ID: <1216136223.487cc41f62a56@webmail.igc.gulbenkian.pt> The Gulbenkian Training Programme in Bioinformatics OEIRAS, PORTUGAL http://gtpb.igc.gulbenkian.pt Deadline for applications: July 30th 2008 Powerful Search and Mining in Biological Databases - PSMBD08 Instructors - Ophir Frieder, Georgetown University, Washington DC, USA - Jay Urbain, Illinois Institute of Technology, Chicago IL, USA Course dates: September 14th - 18th 2008 We introduce the foundations of information systems as they relate to Bioinformatics. We assume no prior knowledge, as we initially overview the principal methods in relational database management systems, information retrieval, and data mining. We describe evaluation approaches and support instruction via hands-on laboratory assignments. This course will serve as an introduction for work in the field and will provide the participants with the fundamental understanding to conduct research in this domain. Target audience: The course was designed to suit a mixed audience of newcomers to Bioinformatics - with or without a biological background, and practitioners that wish to deepen their knowledge in the foundations of information systems, as they apply to the Bioinformatics world. It will also suit power users and software developers. Special attention will be given to Search and Data Mining techniques in the scope of the design, construction and exploration of biological databases. Some of the particular aspects of their implementation in high performace platforms will be covered. Note: We cannot provide scholarships. However we can help in finding very cheap accomodation and food around the Campus, to alleviate tour total costs Contacts: see http://gtpb.igc.gulbenkian.pt Pedro Fernandes, GTPB Coordinator Instituto Gulbenkian de Ciencia, Oeiras, PORTUGAL From ykalidas at gmail.com Tue Jul 15 12:34:56 2008 From: ykalidas at gmail.com (Kalidas Yeturu) Date: Tue, 15 Jul 2008 22:04:56 +0530 Subject: [BiO BB] how to calculate the atom distance between antigen and antibody In-Reply-To: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> References: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> Message-ID: <5632703b0807150934k7e19dc55o4651378332986432@mail.gmail.com> Hi Mr.Li You may use my program 'get_list_of_all_pair_distances.c' to obtain all pair distances between atoms in a given PDB file. The program will output where lines correspond to corresonponding lines in PDB file that have ATOM/HETATM cards; and es are in ascending order. You can select that pair of lines which correspond to the pair of atoms from chains you want to find distance. I checked '1jps.pdb' and noticed that there are 3 chains L, H and T. You may need to tailor the above program to tune the output to your specific need. With Regards Kalidas. Y On Tue, Jul 15, 2008 at 4:27 AM, Xue Li wrote: > hello all, > > I am new in this. > > If I have 1JPS.pdb, would someone please tell me how to calculate the atom > distance between antigen and antibody? > > Thank you. > > Li > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -- Kalidas Y http://ssl.serc.iisc.ernet.in/~kalidas From marchywka at hotmail.com Tue Jul 15 20:38:16 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 15 Jul 2008 20:38:16 -0400 Subject: [BiO BB] how to calculate the atom distance between antigen and antibody In-Reply-To: <0D9D8372-11E1-48A9-AFF2-F6E171C3010D@crs4.it> References: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> <0D9D8372-11E1-48A9-AFF2-F6E171C3010D@crs4.it> Message-ID: > From: floris at crs4.it > To: bbb at bioinformatics.org > Date: Tue, 15 Jul 2008 16:33:26 +0200 > Subject: Re: [BiO BB] how to calculate the atom distance between antigen and antibody > > Hi Li, > > you can do it with PyMol. I was going to mention that many viewers may have some functionality but I couldn't check Cn3d or RasMol. Do you know if PyMol will build under cygwin? Last time I looked it didn't. I would also mention that the pdb files are ascii and, if you just want to pick some random atoms, you could probably use PERL but you'll probably discover you want molecule/cavity surfaces, and then you will want realistic potentials, then you will want ab initio etc.... I have a molecule viewer here with some links to other viewers ( no PyMol or "O" but they are options ), http://www.spottext.com/marchywka/glutp/docs.html that has source code including a pdb class ( terribly hacked from early testing but a good starting point if you want something in c++). I also have cavity code for hard-sphere surfaces in various states of development ( you can see the pictures... ). > > > M. > > > Matteo Floris > > CRS4 Bioinformatica > http://www.bioinformatica.crs4.org > phone: +39 070 9250 422 > fax: +39 070 92433114 > ________________________________ > >> hello all, >> >> I am new in this. >> >> If I have 1JPS.pdb, would someone please tell me how to calculate >> the atom >> distance between antigen and antibody? >> >> Thank you. >> >> Li >> _______________________________________________ >> 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 _________________________________________________________________ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_072008 From me.lixue at gmail.com Wed Jul 16 16:20:08 2008 From: me.lixue at gmail.com (Xue Li) Date: Wed, 16 Jul 2008 15:20:08 -0500 Subject: [BiO BB] how to calculate the atom distance between antigen and antibody In-Reply-To: <5632703b0807150934k7e19dc55o4651378332986432@mail.gmail.com> References: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> <5632703b0807150934k7e19dc55o4651378332986432@mail.gmail.com> Message-ID: <62ed16460807161320i3bbf3a73we23f8c80b24352bc@mail.gmail.com> Thank you guys for replying my email. I think that I did not make myself clear enough. My problem is I do not even know from a pdb file which atoms belongs to antigen and which belongs to antibody. For example, for 1JPS.pdb. There are three chains: chain L, chain H and chain T. Part of the pdb is : ---------------------- HEADER IMMUNE SYSTEM 03-AUG-01 1JPS TITLE CRYSTAL STRUCTURE OF TISSUE FACTOR IN COMPLEX WITH TITLE 2 HUMANIZED FAB D3H44 COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNOGLOBULIN FAB D3H44, LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 FRAGMENT: FAB FRAGMENT; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: IMMUNOGLOBULIN FAB D3H44, HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 FRAGMENT: FAB FRAGMENT; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: TISSUE FACTOR; COMPND 13 CHAIN: T; COMPND 14 FRAGMENT: EXTRACELLULAR DOMAIN; COMPND 15 ENGINEERED: YES ----------------------------------- Is chain T antigen, because chain L and chain H are denoted as LIGHT CHAIN and HEAVY CHAIN? Is this a general rule to tell which chain corresponds to antigen? Thank you very much! Li On Tue, Jul 15, 2008 at 11:34 AM, Kalidas Yeturu wrote: > Hi Mr.Li > You may use my program 'get_list_of_all_pair_distances.c' to obtain all > pair distances between atoms in a given PDB file. The program will output > > where lines correspond to corresonponding lines in PDB file that have > ATOM/HETATM cards; and es are in ascending order. > > You can select that pair of lines which correspond to the pair of atoms > from chains you want to find distance. I checked '1jps.pdb' and noticed > that > there are 3 chains L, H and T. > > You may need to tailor the above program to tune the output to your > specific > need. > > With Regards > Kalidas. Y > > On Tue, Jul 15, 2008 at 4:27 AM, Xue Li wrote: > > > hello all, > > > > I am new in this. > > > > If I have 1JPS.pdb, would someone please tell me how to calculate the > atom > > distance between antigen and antibody? > > > > Thank you. > > > > Li > > _______________________________________________ > > BBB mailing list > > BBB at bioinformatics.org > > http://www.bioinformatics.org/mailman/listinfo/bbb > > > > > > -- > Kalidas Y > http://ssl.serc.iisc.ernet.in/~kalidas > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > > -- Xue, Li Bioinformatics and Computational Biology program Material Science Iowa State University Ames, IA 50010 515-450-7183 From marchywka at hotmail.com Fri Jul 18 05:49:15 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Fri, 18 Jul 2008 05:49:15 -0400 Subject: [BiO BB] how to calculate the atom distance between antigen and antibody In-Reply-To: <62ed16460807161320i3bbf3a73we23f8c80b24352bc@mail.gmail.com> References: <62ed16460807141557h439a53byc5eea1221361c5ca@mail.gmail.com> <5632703b0807150934k7e19dc55o4651378332986432@mail.gmail.com> <62ed16460807161320i3bbf3a73we23f8c80b24352bc@mail.gmail.com> Message-ID: > Date: Wed, 16 Jul 2008 15:20:08 -0500 > From: me.lixue at gmail.com > To: bbb at bioinformatics.org > Subject: Re: [BiO BB] how to calculate the atom distance between antigen and antibody > > Thank you guys for replying my email. > > I think that I did not make myself clear enough. > > My problem is I do not even know from a pdb file which atoms belongs to > antigen and which belongs to antibody. I would suggest using any of the viewers mentioned and just try pointing at a few things. If you go get my source code, I put references in. Maybe these will help, ( in any case, I think pdb.org is the definitive site for this particular file type ) $ grep http atom/pdb* | grep -v "\.bak:" | unix2dos> /dev/clipboard atom/pdb_atom.cpp:// http://www.wwpdb.org/documentation/format3.0-dif.pdf atom/pdb_atom.cpp:// http://bmerc-www.bu.edu/needle-doc/latest/atom-format.html atom/pdb_atom.cpp:// http://www.wwpdb.org/documentation/format23/sect9.html#ATOM atom/pdb_chain_maker.h://http://peds.oxfordjournals.org/cgi/reprint/10/7/777.pdf atom/pdb_chain_maker.h://http://www.umass.edu/microbio/rasmol/rasbonds.htm atom/pdb_chain_maker.h://http://bioinformatics.oxfordjournals.org/cgi/reprint/17/10/949.pdf atom/pdb_chain_maker.h://http://deposit.pdb.org/cc_dict_tut.html > > For example, for 1JPS.pdb. There are three chains: chain L, chain H and > chain T. > > Part of the pdb is : > > ---------------------- > HEADER IMMUNE SYSTEM 03-AUG-01 > 1JPS > TITLE CRYSTAL STRUCTURE OF TISSUE FACTOR IN COMPLEX > WITH > TITLE 2 HUMANIZED FAB > D3H44 > COMPND MOL_ID: > 1; _________________________________________________________________ Keep your kids safer online with Windows Live Family Safety. http://www.windowslive.com/family_safety/overview.html?ocid=TXT_TAGLM_WL_family_safety_072008 From gfogel at natural-selection.com Sat Jul 19 17:56:43 2008 From: gfogel at natural-selection.com (Gary Fogel) Date: Sat, 19 Jul 2008 14:56:43 -0700 Subject: [BiO BB] IEEE CIBCB 2009 Call for Papers Message-ID: <20080719215646.3D52C48E50@agamemnon.xo.com> ----------------------------------------------------------------------------- Call for Papers: IEEE CIBCB 2009 2009 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology March 30-April 2, Nashville, TN, USA ----------------------------------------------------------------------------- This symposium will bring together top researchers, practitioners, and students from around the world to discuss the latest advances in the field of Computational Intelligence and its application to real world problems in biology. Computational Intelligence includes artificial neural networks, fuzzy logic, evolutionary algorithms, and other emerging techniques. Topics of interest include but are not limited to: gene expression array analysis, structure prediction and folding, drug design, molecular sequence alignment and analysis, metabolic pathway analysis, medical imaging and pattern recognition, analysis of large biological data sets, and a variety of other topics. The use of computational intelligence must play a substantial role in submitted papers. Submissions will be peer reviewed and accepted papers will be published in the conference proceedings. Paper Submission: Prospective authors are invited to submit papers of no more than eight (8) pages including results, figures and references; submission details can be found on the symposium web site: www.ieee-ssci.org. Authors are expected to present their paper at the symposium. IEEE CIBCB 2009 will be held in conjunction with the IEEE Symposium Series on Computational Intelligence 2009 (IEEE SSCI 2009). Over 20 such conferences will be co-located at this event. Special Sessions and Tutorials: It is anticipated that the symposium will have a number of special sessions and tutorials. Consult the SSCI symposium web site for instructions on proposing a special session or tutorial. Papers for special sessions must have significant computational intelligence content. Location: Nashville, Tennessee is well known for its cultural events and moderate climate. It is considered a global music center. Nashville is the capital of Tennessee and located on the beautiful Cumberland River. ---------------------------------------------------------------------- Important Dates: Special session and tutorial proposal deadline: August 30, 2008 Paper submission deadline: October 31, 2008 Author notification: November 30, 2008 Camera-ready paper deadline: January 15, 2009 Conference: March 30-April 2, 2009 ---------------------------------------------------------------------- Program Chair: Kay C. Wiese Technical Co-Chairs: Madhu Chetty, Mihail Popescu Publicity Chair: Gary B. Fogel Proceedings Chair: L. Gwenn Volkert Special Sessions Chair: Scott F. Smith Tutorials Chair: Dan Ashlock ---------------------------------------------------------------------- For further inquires: IEEE SSCI 2009 Enquiries: Vincenzo Piuri ? piuri at dti.unimi.it SSCI Symposium Chair IEEE CIBCB 2009 Enquiries: Kay C. Wiese ? wiese at cs.sfu.ca CIBCB Program Chair http://www.ieee-ssci.org http://www.ieee-ssci.org/files/SSCI2009cfp.pdf From scomilmem at yahoo.com Mon Jul 21 11:12:27 2008 From: scomilmem at yahoo.com (sco mil) Date: Mon, 21 Jul 2008 08:12:27 -0700 (PDT) Subject: [BiO BB] Biology search engine Message-ID: <980919.92966.qm@web58007.mail.re3.yahoo.com> Hello BBB members, ? I would like to share this new biology search engine with you, which has search categories for bioinformatics?software and online tools. ? www.vadlo.com ? Thought you might be interested and I hope you find it useful! ? Scott From suryabioinfo at yahoo.com Wed Jul 23 06:44:45 2008 From: suryabioinfo at yahoo.com (Surya Gaya) Date: Wed, 23 Jul 2008 03:44:45 -0700 (PDT) Subject: [BiO BB] about detection calls and signal values.. Message-ID: <394573.79134.qm@web59805.mail.ac4.yahoo.com> hi , i used dChip recently and got the results in which i have the probe sets. i want to know the gene names of those probe sets. can somebody please tell me where can i get them and how? thanks in advance. and i also want to know about the detection calls and signal values..what are they? how are they attained? what do they signify and how? how are they supposed to be interpreted? please suggest any links aswell that could be of useful information to me. thank you so much group... surya. From marchywka at hotmail.com Sat Jul 26 15:30:13 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Sat, 26 Jul 2008 15:30:13 -0400 Subject: [BiO BB] looking for conserved domain downloadable databases. Message-ID: Hi, I was trying to find something like the prosite rules database that may be include more conserved domains. That is, I've got a bunch of short peptides and I want to determine if any of them have functional significance. I would imagine that function prediction servers may have such database but probably not in downloadable form. In particular, I took about 3000 short sequences that have something to do with cell cycle arrest ( eutilsnew is my own script but you get the idea), eutilsnew -protein -v -out stuff '"cell cycle" arrest' $progpath/file_parsing -fastas stuff stuff_fasta I have a way to get the most frequently occuring short strings. In this case, I got some interesting hits, ( and also found out that "M" occurs at the start quite often, adding some confidence that the code is running properly...) $progpath/string_test -fastas stuff_fasta -status -conserved | grep [A-Z] | sort -g -r -k 2 > cca_roots $ head cca_roots M 2321 PENL 565 L 545 FENL 461 YENL 458 F 456 W 455 WENL 454 MS 425 RSPS 396 In any case, I wanted to see if the regular expression [PFYW]ENL means anything. First, I did get a control group, ( only got the first 1500 and used ctrl-c to "select" the first few), eutilsnew -v -protein -out some_hydo "hydroxylase" $ head hydro_roots M 1418 GDAA 312 GAGL 308 DAAH 299 AGLL 283 GLLS 266 IGLA 263 PVAG 258 LLSS 253 AGQG 253 The prosite rule list that I have shows some "ENL" candidates explicitly( non of which include PWY or W as a leading acid ) and maybe more that are more cryptic, $ grep ENL /cygdrive/c/mydocs/scripts/cc/affx/prosite_rules P.{2}[LIVMF]{2}[LIVMS].[GDN].{3}[DENL].{3}[LIVM].E.{4}[GNQKRH][LIVM][AP]>rule|216|PEPDTIDE Prosite RIBOSOMAL_S2_2 K[LIVMF]DG[LIVMAS][SAG].{4}Y.{2}[GRD].[LF].{4}[ST]RG[DN]G.{2}G[DE][DENL]>rule|832|PEPDTIDE Prosite DNA_LIGASE_N1 CC[SHYN].{0,1}[PRG][RPATV]C[ARMFTNHG].{0,4}[QWHDGENLFYVP][RIVYLGSDW]C>rule|1104 |PEPDTIDE Prosite ALPHA_CONOTOXIN but that is all I have to go on. I did a quick look at NCBI CDART and related pfam resources but couldn't figure out how to download anything useful. I couldn't immediately get blast to return any hits on "ENL" and I'm not sure what all parameters I'd need to tweak to search on short things. Thanks. Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 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. _________________________________________________________________ Time for vacation? WIN what you need- enter now! http://www.gowindowslive.com/summergiveaway/?ocid=tag_jlyhm From hformadi at vbi.vt.edu Fri Jul 25 21:18:18 2008 From: hformadi at vbi.vt.edu (Herman Formadi) Date: Fri, 25 Jul 2008 21:18:18 -0400 Subject: [BiO BB] Biology search engine In-Reply-To: <980919.92966.qm@web58007.mail.re3.yahoo.com> References: <980919.92966.qm@web58007.mail.re3.yahoo.com> Message-ID: <488A7B5A.2090903@vbi.vt.edu> Thanks, Hermansco mil wrote: > Hello BBB members, > > I would like to share this new biology search engine with you, which has search categories for bioinformatics software and online tools. > > www.vadlo.com > > Thought you might be interested and I hope you find it useful! > > Scott > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > From s_uchida21 at yahoo.co.jp Sun Jul 27 09:36:09 2008 From: s_uchida21 at yahoo.co.jp (=?ISO-2022-JP?B?GyRCRmJFRBsoQiAbJEJMdzpIGyhC?=) Date: Sun, 27 Jul 2008 22:36:09 +0900 (JST) Subject: [BiO BB] about detection calls and signal values.. In-Reply-To: <394573.79134.qm@web59805.mail.ac4.yahoo.com> Message-ID: <20080727133609.28406.qmail@web3909.mail.bbt.yahoo.co.jp> Hi Surya: About your questions, it is better to read information at Bioconductor.org. http://www.bioconductor.org/ You will find answers to most of your questions. Instead of dChip, I highly recommend using RMA through Affy and moderate t-statistics through limma; both algorithms are implemented in R. Shizuka --- Surya Gaya wrote: > hi , > i used dChip recently and got the results in > which i have the probe > sets. i want to know the gene names of those > probe sets. can somebody > please tell me where can i get them and how? > thanks in advance. > > and i also want to know about the detection > calls and signal values..what are they? how are > they attained? what do they signify and how? > how are they supposed to be interpreted? please > suggest any links aswell that could be of > useful information to me. > thank you so much group... > surya. > > > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb > -------------------------------------- Power up the Internet with Yahoo! Toolbar. http://pr.mail.yahoo.co.jp/toolbar/ From pete at softgenetics.com Sat Jul 26 15:41:34 2008 From: pete at softgenetics.com (Pete Marchetto) Date: Sat, 26 Jul 2008 15:41:34 -0400 Subject: [BiO BB] Fwd: MySQL performance tuning References: Message-ID: Pete Marchetto Staff Scientist SoftGenetics, LLC http://softgenetics.com/ Begin forwarded message: > Date: July 26, 2008 4:11:35 PM EDT > Subject: MySQL performance tuning > Source: Hackszine.com > Author: Jason Striegel > > Jay Pipes, MySQL employee and co-author Pro MySQL, gave a great > presentation to Google employees which covers a number of techniques > for tuning performance on MySQL. His examples include debugging and > analyzing problems as well as best practices for table and index > design, query and join operations, and server variable adjustments. > > It's a little over 40 minutes long, but incredibly informative, > whether you're a casual querier or a power MySQL user. Though some > of this stuff is MySQL (or MyISAM or InnoDB) specific, the majority > of the content is essential material for the average database > application developer. > > If you don't have time to sit through it (shame on you) or you're > looking to jump right to a specific topic, there's a nice time-coded > dissection of the talk over at Peteris Krumins' blog. There's > something so appropriate about adding a search index to a video > about MySQL optimization. > > Performance Tuning Best Practices for MySQL > Video Index > > Read more? > From codeshepherd at gmail.com Mon Jul 28 13:15:14 2008 From: codeshepherd at gmail.com (Deepan Chakravarthy) Date: Mon, 28 Jul 2008 22:45:14 +0530 Subject: [BiO BB] Biology search engine In-Reply-To: <488A7B5A.2090903@vbi.vt.edu> References: <980919.92966.qm@web58007.mail.re3.yahoo.com> <488A7B5A.2090903@vbi.vt.edu> Message-ID: Bioask (http://www.bioask.com/) is another biology search engine with wonderful features like entity relationship maps, sequence details for related entities, etc. On 26-Jul-08, at 6:48 AM, Herman Formadi wrote: > Thanks, > > Hermansco mil wrote: >> Hello BBB members, >> >> I would like to share this new biology search engine with you, >> which has search categories for bioinformatics software and online >> tools. >> >> www.vadlo.com >> >> Thought you might be interested and I hope you find it useful! >> >> Scott >> >> >> >> _______________________________________________ >> 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 From Lambert at Chatham.edu Mon Jul 28 15:36:35 2008 From: Lambert at Chatham.edu (Lambert, Lisa) Date: Mon, 28 Jul 2008 15:36:35 -0400 Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter In-Reply-To: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E111@MAILBOX.chatham.local> References: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E111@MAILBOX.chatham.local> Message-ID: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E112@MAILBOX.chatham.local> While comparing the promoters of a set of genes with similar metabolic functions, I came across a region of around 270 bp that was present in nine of the genes. I found this same region in the same spot in the higher primates, but in no other species. The lowest percent identity between genes is 69% and the highest is 86%. I wanted to see if this region was associated with other genes, but then I ran into a problem. When I try to do BLAT or BLASTN genomic searches, I get a lot of "noise," especially with short, exact hits. Changing the parameters at ENTREZ typically yields either a handful of hits, or well over 150,000. ENSEMBL will return hits of 10 bp with 100% identity while missing 250 bp with 75% identity. What I really is an engine where I can specify that only hits longer than 200 bp with an identity of at least 50% be returned. Does anyone know of a tool that will do this? Lisa Lambert Chatham University Pittsburgh, PA From marchywka at hotmail.com Tue Jul 29 03:08:04 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Tue, 29 Jul 2008 03:08:04 -0400 Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter In-Reply-To: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E112@MAILBOX.chatham.local> References: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E111@MAILBOX.chatham.local> <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E112@MAILBOX.chatham.local> Message-ID: > From: Lambert at Chatham.edu > To: bbb at bioinformatics.org > Date: Mon, 28 Jul 2008 15:36:35 -0400 > Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter > >[...]What I really is an engine where I can specify that only hits longer than 200 bp with an identity of at least 50% be returned. Does anyone know of a tool that will do this? In the past, I've written scripts to download search results non-selectively and then sort through them locally with custom criteria. I'm a programmer so this is my approach to everything but I think it makes sense whenever you expect to do a lot of ad hoc or exploratory processing. One of the well know packages, I think people keep mentioning bioperl, may be worth considering rather than hoping to find a specific search engine that does exactly what you want. In my case, I was looking for 25bp long DNA sequences and wanted to find "what is close by" in various species. IIRC, the things I hoped to find "close by" were sequences close to different 25bp probes in my query list. So, I did blast searches on genomes and then extracted the hit locations, requested expanded versions of the approriate chromosomes, and fiddled with the results using text processing scripts. I guess effectively I had a query that looked like, " find areas that contain 10, 25bp sequences in any order, with matches being better than 20/25 for each key sequence, and not more than about 300bp in total span." Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 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. > _________________________________________________________________ Time for vacation? WIN what you need- enter now! http://www.gowindowslive.com/summergiveaway/?ocid=tag_jlyhm From mmuratet at hudsonalpha.com Mon Jul 28 16:23:35 2008 From: mmuratet at hudsonalpha.com (Michael Muratet) Date: Mon, 28 Jul 2008 15:23:35 -0500 Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter In-Reply-To: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E112@MAILBOX.chatham.local> References: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E111@MAILBOX.chatham.local> <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E112@MAILBOX.chatham.local> Message-ID: <6C78A04E-CA6A-4DAF-8527-CA408B2EABE3@hudsonalpha.org> Lisa I believe the vmatch tool (a suffix array algorithm) has inputs that will handle that. I have used it for searching for pri-miRNAs where I wanted things in particular range of lengths. I can't remember the exact URL to get it, but a Google search will turn it up. Regards Mike On Jul 28, 2008, at 2:36 PM, Lambert, Lisa wrote: > While comparing the promoters of a set of genes with similar > metabolic functions, I came across a region of around 270 bp that > was present in nine of the genes. I found this same region in the > same spot in the higher primates, but in no other species. The > lowest percent identity between genes is 69% and the highest is 86%. > I wanted to see if this region was associated with other genes, but > then I ran into a problem. When I try to do BLAT or BLASTN genomic > searches, I get a lot of "noise," especially with short, exact hits. > Changing the parameters at ENTREZ typically yields either a handful > of hits, or well over 150,000. ENSEMBL will return hits of 10 bp > with 100% identity while missing 250 bp with 75% identity. What I > really is an engine where I can specify that only hits longer than > 200 bp with an identity of at least 50% be returned. Does anyone > know of a tool that will do this? > > Lisa Lambert > Chatham University > Pittsburgh, PA > > _______________________________________________ > BBB mailing list > BBB at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bbb From Sterten at aol.com Mon Jul 28 17:38:45 2008 From: Sterten at aol.com (Sterten at aol.com) Date: Mon, 28 Jul 2008 17:38:45 EDT Subject: [BiO BB] Looking for a DNA search engine that includes length as a parame... Message-ID: can't you save the many hits to a file and then run refined searches on that file ? From bony_chatt at yahoo.com Tue Jul 29 07:39:08 2008 From: bony_chatt at yahoo.com (bony chatterjee) Date: Tue, 29 Jul 2008 04:39:08 -0700 (PDT) Subject: [BiO BB] Which one the best step after M.Sc----please help Message-ID: <668069.28123.qm@web51804.mail.re2.yahoo.com> Hi, I'm basically from Kolkata (calcutta) , India but I'm doing M.Sc in Bioinformatics from Annamalai University of south India (last semester) in distance mode. After this I want to do Ph.D in genomics or functional genomics or drug design or bioinformatics. from where I will do that in India or in USA? It is possible to PhD in distance mode? If yes, then from where? ? I want to ba a professional in these fields. Can you tell me the name and address of some reputed institutes (In India) who conduct industry oriented courses on Bioinformatics / Functional Genomics / Drug Desigining? From Lambert at Chatham.edu Tue Jul 29 09:08:04 2008 From: Lambert at Chatham.edu (Lambert, Lisa) Date: Tue, 29 Jul 2008 09:08:04 -0400 Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter Message-ID: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E116@MAILBOX.chatham.local> Thanks, Mike I've used PERL (I'll definitely take a look at BIOPERL), and could write something that locally searches downloaded FASTA results or whole genome files. I was just hoping I had missed something faster, since this is more of a side project than my main area of interest. It might be a good student project for the fall! It also occurred to me (after sleeping on it) that, given the size, these might be SINEs, so I'm going to check Repeatmaster and see if I can narrow things that way. Lisa ________________________________________ From: bbb-bounces at bioinformatics.org [bbb-bounces at bioinformatics.org] On Behalf Of Mike Marchywka [marchywka at hotmail.com] Sent: Tuesday, July 29, 2008 3:08 AM To: General Forum at Bioinformatics.Org Subject: Re: [BiO BB] Looking for a DNA search engine that includes length as a parameter > From: Lambert at Chatham.edu > To: bbb at bioinformatics.org > Date: Mon, 28 Jul 2008 15:36:35 -0400 > Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter > >[...]What I really is an engine where I can specify that only hits longer than 200 bp with an identity of at least 50% be returned. Does anyone know of a tool that will do this? In the past, I've written scripts to download search results non-selectively and then sort through them locally with custom criteria. I'm a programmer so this is my approach to everything but I think it makes sense whenever you expect to do a lot of ad hoc or exploratory processing. One of the well know packages, I think people keep mentioning bioperl, may be worth considering rather than hoping to find a specific search engine that does exactly what you want. In my case, I was looking for 25bp long DNA sequences and wanted to find "what is close by" in various species. IIRC, the things I hoped to find "close by" were sequences close to different 25bp probes in my query list. So, I did blast searches on genomes and then extracted the hit locations, requested expanded versions of the approriate chromosomes, and fiddled with the results using text processing scripts. I guess effectively I had a query that looked like, " find areas that contain 10, 25bp sequences in any order, with matches being better than 20/25 for each key sequence, and not more than about 300bp in total span." Mike Marchywka 586 Saint James Walk Marietta GA 30067-7165 415-264-8477 (w)<- use this 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. > _________________________________________________________________ Time for vacation? WIN what you need- enter now! http://www.gowindowslive.com/summergiveaway/?ocid=tag_jlyhm _______________________________________________ BBB mailing list BBB at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bbb From marchywka at hotmail.com Wed Jul 30 07:26:27 2008 From: marchywka at hotmail.com (Mike Marchywka) Date: Wed, 30 Jul 2008 07:26:27 -0400 Subject: [BiO BB] Looking for a DNA search engine that includes length as a parameter In-Reply-To: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E116@MAILBOX.chatham.local> References: <370F994DA14AF6449AA6A1FFCBDF6D9365E4B8E116@MAILBOX.chatham.local> Message-ID: > From: Lambert at Chatham.edu > To: bbb at bioinformatics.org > Date: Tue, 29 Jul 2008 09:08:04 -0400 > Subject: Re: [BiO BB] Looking for a DNA search engine that includes length as a parameter > > Thanks, Mike > > I've used PERL (I'll definitely take a look at BIOPERL), and could write something that locally searches downloaded FASTA results or whole genome files. I was just hoping I had missed something faster, since this is more of a side project than my main area of interest. It might be a good student project for the fall! > I was going to suggest that at some point it may be faster to download entire genomes and write your own brute force or custom indexing code. At least on cygwin, I did find various limitations both in PERL and C++ that created important speed problems so implementation issues could be important to getting results while you still care or not :) Usually it is pretty obvious that you hit an IO or virtual memory problem and just changing format and using some bash utilities really helped ( I guess you could store genomes in gzip format and decompress on-the-fly as one example that may be faster than reading plain ascii files in some cases). I think with PERL the hashes are great until they got too big for physical memory then everything pretty much stops. > It also occurred to me (after sleeping on it) that, given the size, these might be SINEs, so I'm going to check Repeatmaster and see if I can narrow things that way. > > > Mike Marchywka > 586 Saint James Walk > Marietta GA 30067-7165 > 415-264-8477 (w)<- use this > 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. > > > >> > _________________________________________________________________ > Time for vacation? WIN what you need- enter now! > http://www.gowindowslive.com/summergiveaway/?ocid=tag_jlyhm > _______________________________________________ > 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 _________________________________________________________________ Use video conversation to talk face-to-face with Windows Live Messenger. http://www.windowslive.com/messenger/connect_your_way.html?ocid=TXT_TAGLM_WL_Refresh_messenger_video_072008