NRSP-8 Bioinformatics/Database Update # 1

March 1, 2005

  1. Development of Pig QTL database
  2. Development of a PCR primer development tool
  3. Development of a livestock sequence Blast server
  4. The Aquaculture genomics web site has a new home and look
  5. Suggestion for new projects
  6. Upcoming bioinformatics meetings (16 items)
  7. Upcoming short courses (5 items)

Development of Pig QTL database. The pig quantitative trait loci (QTL) database (PigQTLdb) has been well used since its release last December ( http://www.animalgenome.org/QTLdb/ ). On average about 6,000 web hits per month were made to PigQTLdb. The database contains all pig QTL data published during the past 10+ years. The database and its peripheral tools were made to compare, confirm, and locate on pig chromosomes the most feasible location for a candidate gene responsible for quantitative trait(s) important to pig production. To date, 791 QTL from 73 publications have been curated into the database. Please contact Zhiliang Hu (z...@iastate.edu) with any suggested improvements or additional data to add to the database.

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Development of a PCR primer development tool. The Expeditor tool has received some good comments and been used by some 200+ users since its release last October ( http://www.genome.iastate.edu/hu/expeditor ). Expeditor is a web-based tool which combines human intron/exon structural information and EST sequence information of the target species to design primers for amplification of genomic segments of a given gene.

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Development of a livestock sequence Blast server. A NAGRP Blast Server is now in service ( http://www.animalgenome.org/blast/ ). This blast server uses a local copy of NCBI blast suite, which includes bl2seq, blastall, megablast, blastpgp, blastclust, netblast, etc. The local sequence data sets include all non-human, non-mouse EST sequences from the Genbank, Whole Genome Shotgun (WGS) sequence assemblies for different organisms from Genbank. These data sets are updated from Genbank every night. The local sequence data sets also include TIGR Gene Indices for Cattle, Chicken, Pig, Salmon, Catfish, and Rainbow Trout. The TIGR Indices are updated weekly (done every Saturday night). Currently users can use the web server for their blast. Links to the blast server are included on each of the species pages under resources. We can develop a service portal for batch blast if there are such needs in the community. Please email Jre...@iastate.edu to discuss.

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The Aquaculture genomics web site has a new home and look. The URL to the current web site is http://www.genome.iastate.edu/aquaculture/ . Please send information that you would like added to Rexroad, Caird (crexroad@ncccwa.ars.usda.gov) or Zhiliang Hu (z...@iastate.edu).

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New projects: As always if you have suggestions about what needs to be developed/improved or how we can help please do not hesitate to contact us. Jre...@iastate.edu

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UPCOMING BIOINFORMATICS MEETINGS (see http://www.genome.iastate.edu/community/meetings.html for more details)
  1. March 19-23, 2005 - 3rd Symposium on Computational Cell Biology Web: http://www.ccbsymposium.org/index.html Place: Cranwell Resort & Golf Club, Lenox, MA
  2. April 8-13, 2005 - Keystone Symposia: Proteomics and Bioinformatics Web: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=734 Place: Keystone, Colorado, USA
  3. April 24-25, 2005 - Computational Challenges in Systems Biology Web: http://www.systemsbiology.org/symposium2005/ Organized by Institute for Systems Biology Place: Seattle
  4. May 17-19, 2005 - Bio-IT World Conference & Expo Web: http://www.bioitworldexpo.com/ Organized by IDG World Expo Place: Hynes Convention Center, Boston
  5. June 9-12, 2005 - 7th International Conference on Bioinformatics 2005 Web: http://bioinfo.ebc.ee/bio2005/indexen.php Place: Tartu, Estonia
  6. June 17, 2005 - Bioinformatics: Knowledge Discovery in Biology 2005 Web: http://xldb.fc.ul.pt/bkdb2005/ Place: Lisboa, Portugal
  7. June 25- 29, 2005 - Intelligent Systems for Molecular Biology (ISMB 2005) Web: http://www.iscb.org/ismb2005/ Location: Detroit, Michigan Satellite event (June 24, 2005): Eighth Annual Bio-Ontologies Meeting Web: http://bio-ontologies.man.ac.uk/ Submission Deadline: 29th April 2005
  8. June 31-5, 2005 - 14th International Conference on Cytochromes P450: Biochemistry, Biophysics, and Bioinformatics Web: http://www.p450dallas2005.us/ Place: UT Southwestern Medical Center, Dallas
  9. July 10-13, 2005 - 9th World Multi-Conference on Systemics, Cybernetics and Informatics Web: ( http://www.iiisci.org/sci2005 ), which will Place: Orlando, Florida
  10. July 21-26, 2005 - 6th International Symposium on Computational Biology and Genome Informatics Web: http://www.jcis.org/pages/subconference/cbgi/cbgi.aspx Place: Marriott City Center, Salt Lake City, CO
  11. August 8-11, 2005 - IEEE Computational Systems Bioinformatics Conference (CSB 2005) Web: http://conferences.computer.org/bioinformatics/ Place: Stanford, CA
  12. August 22-25, 2005 - 5th International Workshop on Bioinformatics and Systems Biology (IBSS 2005) Web: http://www.biologie.hu-berlin.de/~gk/events/ibsb2005/index.htm Place: Berlin, Germany
  13. September 22-25, 2005 - Integration of Structural and Functional Genomics Web: http://www.bb.iastate.edu/%7Egfst/homepg.html Place: Ames, Iowa
  14. September 28 - October 1, 2005 - 4th European Conference on Computational Biology (ECCB/05) Web: http://www.eccb05.org/ Place: Madrid
  15. October 26-30, 2005 - Genome Informatics Web: http://meetings.cshl.edu/meetings/info05.shtml Organized by CSHL Place: Cold Spring Harbor
  16. November 14-15, 2005 - Computational Intelligence in Bioinformatics and Computational Biology Web: http://www.cibcb.org/ Organized by IEEE Computational Intelligence Society San Diego, California

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UPCOMING SHORT COURSES (see http://www.genome.iastate.edu/edu/short_courses/ for details)
  1. Fortran programming and Bayesian implementation via Markov Chain Monte Carlo (MCMC) techniques Time: May 16-27, 2005 Location: Department of Animal and Dairy Science, University of Georgia Lecturer: Romdhane Rekaya and Ignacy Misztal
  2. ASREML Workshop Time: June 13-14, 2005 Location: Iowa State University, Ames, IA Lecturer: Steve Kachman, University of Nebraska
  3. C++ Programming for Animal Breeding Time: June 15-24 Location: Iowa State University, Ames, IA Lecturer: Steve Kachman (Nebraska) and Rohan Fernando (Iowa State)
  4. Design and Analysis of Microarray Experiments Time: July 11-12 Location: Iowa State University, Ames, IA Lecturer: Dan Nettleton (Dept. Statistics, Iowa State)
  5. NCBI PowerScripting Time: April 20-22, 2005 Location: Lister Hill Center (Bldg 38A), NLM, NIH, Bethesda, MD Lecturer: Andrei Gabrielian, Eric Sayers, and David Wheeler Scopes: A 3-day course including both lectures and computer workshops on effectively using the NCBI E-utilities within scripts to automate search and retrieval operations across the entire suite of Entrez databases.

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Items for the next update can be sent to me by no later than May 15 please. 
                    James Reecy
                    U.S. Database/Bioinformatics Coordinator
                    2255 Kildee Hall
                    Department of Animal Science
                    Iowa State University
                    Ames, Iowa 50011-3150 
                    Phone: 515-294-9269 
                    Fax: 515-294-2401
                    Jre...@iastate.edu
                    http://www.genome.iastate.edu

 

NAGRP Bioinformatics Coordination Program
sponsored by the USDA/CSREES NRSP-8
 http://www.genome.iastate.edu/
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