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Pig Genome Newsletter #097
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #97
Date: Tue, 30 Jun 2009 20:46:09 -0500
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************** No. 97 **************
* *
* <angenmap@animalgenome.org> *
* July 1, 2009 *
**************************************
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1. Join the Swine Genome Sequencing Consortium (SGSC) and Pig Genome III
2. Swine Genome Community feedback is needed
3. Illumina and the International Porcine SNP Chip Consortium are pleased
to announce that the porcine 50K+ SNP panel is available
4. The NRSP-8 Bioinformatics Coordination team recently met
5. PAG XVII, January 10-14, 2009 was a great success
6. Help our pork producers
7. Please provide your input
8. Upcoming meetings ( 4 items )
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Join the Swine Genome Sequencing Consortium (SGSC) and Pig Genome III
meeting to celebrate the completion of the pig genome sequence in
Hinxton, UK November 2-4. In anticipation of the completion of the pig
genome sequencing project, this workshop will be “SGSC - the genome
assembly and annotation Pig Genome III: Exploiting the sequence”.
There will be a call for abstracts and registration information in July.
Interested parties should contact either Larry Schook (schook@illinois.edu)
or Martien Groenen (Martien.Groenen@wur.nl).
Swine Genome Community feedback is needed: 1) The Ensembl team has taken
the Pig assembly and plans to run the automated Genebuild. The timeframe
is expected to be 5 months as it is not an easy process. This will add Pig
to the list of species found on the Ensembl website. The best QC for the
analysis will be feedback from the community and we would like lots of it!
Guidance to problematic areas means they can then be corrected in time
for a second Genebuild upon completion of the project; 2) Manual annotation
for some clones is a possibility, but resources are limited. Therefore,
it would be hugely beneficial for the community to identify any sequenced
clone that would benefit from increased annotation provided by manual
intervention and 3) One advantage of opting for the BAC by BAC sequencing
approach was to allow targeted sequencing of important regions first.
These regions identified by the swine community are sequenced as "Top
Priorities" and allow rapid sequence feedback to the community long before
completion of the project. So far, 28 regions of interest have been
prioritized spanning 518 clones or ~3% of the genome. If you know of a
region that would benefit from prioritized sequencing, please email
pig-help@sanger.ac.uk . The deadline is immediate to send a request
carol@sanger.ac.uk (kindly provided by Richard Clark and Carol Churcher).
o o o o o o o o o o o
Illumina and the International Porcine SNP Chip Consortium are pleased
to announce that the porcine 50K+ SNP panel is available and being
shipped. If you did not place an order please do not hesitate to
contact Illumina for further information or questions at
http://www.illumina.com/contactMe.ilmn?CS=1.
o o o o o o o o o o o
The NRSP-8 Bioinformatics Coordination team recently met to discuss ways
to improve both the tools made available and the opportunities to use
them. Please watch the web site (http://www.animalgenome.org/) for new
developments including tools to analyze the pig high density SNP chip.
o o o o o o o o o o o
PAG XVII, January 10-14, 2009 was a great success. The abstracts are
now posted on the web. See http://www.intl-pag.org/ for more
information. Planning is well underway for next year and your
involvement is encouraged.
o o o o o o o o o o o
Help our pork producers. Low pork prices and high inputs have made for
a bad year for many pork producers. This was further fueled by the so
called outbreak of “swine” flu. You can help!! Light up the grill
and buy lots of chops, ribs and brats and enjoy the summer.
o o o o o o o o o o o
Please provide your input The Pig Genome Coordinator is always glad to
hear from NRSP-8 members and other readers about ways to improve the
coordination effort or provide resources that are needed and with which
the coordination program can help
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
2nd Annual NSF-funded Short Course on Statistical Genetics & Statistical
Genomics, July 13-17, 2009, Hilton Hawaiian Village Beach Resort & Spa,
Honolulu, Hawaii. Register at
http://www.soph.uab.edu/ssg/nsfstatgen/nsfsecondannual
7th U.C. Davis Transgenic Animal Research Conf., Aug. 17-22, 2009,
Granlibakken Resort and Conference Center, Tahoe City, CA. See
http://conferences.ucdavis.edu/transgenic
Next generation sequencing: challenges and opportunities. October 1-3,
2009, Casa Convalescencia, Barcelona, Spain http://ngs2009.uab.es
Plant & Animal Genome Conference, PAG XVIII, Jan. 9-13, 2010, Town &
Country Hotel, San Diego, CA. Information available at http://www.intl-
pag.org/ .
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Items for Pig Genome Update 98 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
mfrothsc@iastate.edu
http://www.animalgenome.org/pigs/
cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS
===========================================================================
U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Paid for by funds from the NRSP-8 | Web: http://www.animalgenome.org/pig
| USDA/CSREES sponsored Pig Genome | Mail: angenmap@animalgenome.org
| Coordination Program |
+-----------------------------------+--------------------------------------
