Pig Genome Update No. 79

July 1, 2006

  1. Pig genome sequencing is on the move
  2. Bioinformatics utility tool box/Genomic software archive
  3. Animal QTLdb
  4. Planning for next year's PAG is moving along well
  5. New swine oligo arrays nearing reality
  6. Please provide your input
  7. 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.


Bioinformatics utility tool box/Genomic software archive. A bioinformatics utility tool box is set up at the NAGRP Bioinformatics site. Currently there are 6 utility tools in the "tool box" http://www.animalgenome.org/bioinfo/resources/util/ In addition, publicly available genomics software can be obtained from http://db.genome.iastate.edu/ftp/share/ . Furthermore the livestock blast server can be accessed at http://www.animalgenome.org/blast/ .


Animal QTLdb. The NAGRP Bioinformatics group has been actively working on upgrading the QTL database (formerly known as PigQTLdb) to include more QTL data from multiple species, in part, to build a basis for cross-species comparative QTL studies. The upgrading includes both data updates and software improvements. While the existing curator tool functions are improved, we are adding an internal data viewer and a data review tool for the editors to examine the data after initial curation by curators. The internal data viewer will allow new data to be viewed and/or compared to other published data in a private environment before it may be released to public, and the data owner will have the option to decide on his/her data release to public. We anticipate the release of the set of new tools to public in the coming months. http://www.animalgenome.org/QTLdb/faq.html


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 September 1 newsletter.


Please provide your input. The Swine genome Coordinator is always glad to hear from NRSP-8 members and other readers about ways that the coordination effort can be improved or provide resources that are needed and with which the coordinator can be of help. Also, let him know if you have items of general interest to the swine genetics community that we can include in this Newsletter.


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

Items for Pig Genome Update 80 can be sent to me by no later than August 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
Pig Genome Coordination Program
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