Pig Genome Update No. 78

May 1, 2006

  1. Pig genome sequencing is on the move
  2. Planning for next year's PAG is moving along well
  3. New swine oligo arrays nearing reality
  4. USDA CSREES FY 2006 National Research Initiative information
  5. New bioinformatic tools and materials are available
  6. Upcoming meetings

Pig genome sequencing is on the move. Sequencing has already begun and updates can be seen daily at http://www.animalgenome.org/pigs/genomesequence/ . These updates are provided as part of the Bioinformatic Coordinator's team effort. Other information about the sequencing can be seen at that page and web pages at the Sanger Institute and the University of Illinois.


Planning for next year's PAG is moving along well with a number of exciting speakers already lined up. Anyone with suggestions about PAG-XV speakers or other aspects of PAG should contact PAG animal reps, including Hans Cheng, Max Rothschild, Claire Gill, Mary Delany, Michel Georges and Jim Reecy.


New swine oligo arrays nearing reality. Work continues to get the production of the array materials ready and despite some setbacks they are nearing reality. These should be available this summer and details for obtaining them will be made available in the July 1 newsletter.


USDA CSREES FY 2006 National Research Initiative (competitive grant program) information can be found at http://www.csrees.usda.gov/fo/fundview.cfm?fonum=3D1112 . Total FY 2006 NRI funding was estimated at $183M, but this will likely be reduced by across the board cuts of 1% (to end up at about the same level as last year). Note that there are some changes in the FY2006 NRI. The Program 43.0, Animal Genome, has been divided into Applied Animal Genomics, Tools and Reagents, Bioinformatics, and Functional Genomics. (Functional Genomics will appear on alternate years beginning in FY 2006.) The due date for all is June 15, 2006. As mentioned in a previous issue and discussed again at PAG-XIV, CSREES officials are concerned about the low overall NRI success rate (14 of 73 proposals funded in the 2005 Animal Genome Program or 19%). Efforts (sometimes controversial) have been made to focus the NRI RFA to reduce the effort going into preparing and reviewing unsuccessful proposals.


New bioinformatic tools and materials are available. The first is the "Bioinformatics utility tool box" which is set up at the NAGRP Bioinformatics site. Currently there are 6 utility tools in the "box": 1. Expeditor: Design primers using gene structure and EST information from different species. 2. Prim2: Design primers on the consensus of 2 similar sequences. 3. A sequence alignment diagram drawing tool. 4. Gene ontology (GO) terms classifications counter. 5. DNA Sequence Reverse Complement Converter. 6. Query the Bovine SNP Database by blast. URL: http://www.animalgenome.org/bioinfo/resources/util/ . These tools should help all researchers. The second is the Animal Genomics Software Archive which is an animal genomics software archive site for publicly shared software (http://db.genome.iastate.edu/ftp/share/ ). Those who wish to share their software with the community, please feel free to contact bioinfo- team@animalgenome.org for information on how to deposit your software to this archive.


Upcoming meetings (see: http://www.animalgenome.org/pigs/community/meetings.html )

Items for Pig Genome Update 79 can be sent to me by no later than June 15 please.

                    Max Rothschild
                    U.S. Pig Genome Coordinator
                    2255 Kildee Hall, Department of Animal Science
                    Iowa State University
                    Ames, Iowa 50011
                    Phone: 515-294-6202, Fax: 515-294-2401

cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS

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USDA/CSREES sponsored
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