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Pig Genome Newsletter #095
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #95
Date: Fri, 27 Feb 2009 16:17:32 -0600
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. 95 **************
* *
* <angenmap@animalgenome.org> *
* March 1, 2009 *
**************************************
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1. Sequencing Project Progress is on target to complete in 2009 but needs
your inputs
2. With the renewal of a new NRSP-8 project, members are encouraged to
provide input to the NRSP-8 Bioinformatics coordination team
3. Illumina and the International Porcine SNP Chip Consortium are pleased
to announce that the porcine 50K+ SNP panel is available
4. A Banff Swine Genomics Workshop was held to further engage Canadian
scientists and industry personnel
5. PAG XVII, January 10-14, 2009 was a great success
6. USDA Grant update
7. Please provide your input to the Pig Genome Coordinator.
8. Upcoming meetings ( 8 items )
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Sequencing Project Progress is on target to complete in 2009 but needs
your inputs. The Pig X chromosome sequencing project is making
excellent progress through the sequencing pipeline at the Sanger
Institute, with unfinished sequence data now available for over 750
clones. As the large genome finishing teams begin work to ensure the
finished sequence meets our usual high standard of accuracy, discussions
are underway within the Finishing Department to set finishing guidelines
for these clones. In order to increase the efficiency of the finishing
process we are considering whether to continue tagging regions where the
data are derived only from a single sub-clone. Currently, these tags
appear as miscellaneous feature tags in the EMBL headers, to indicate to
researchers that the region tagged does not conform to the usual
standard as described in the header. This sequence was finished as
follows unless otherwise noted: all regions were either double-stranded
or sequenced with an alternate chemistry or covered by high quality data
(i.e., phred quality >= 30); an attempt was made to resolve all
sequencing problems, such as compressions and repeats; all regions were
covered by at least one sub-clone; and the assembly was confirmed by
restriction digest, except on the rare occasion of the clone being a
YAC. If we no longer asked finishers to scrutinize and tag these
regions we would speed up the finishing process. We don't believe that
this would introduce inaccuracies in the finished sequence, but are
currently carrying out checks to ensure this is the case. We would also
appreciate hearing from anyone who uses the finished sequence to let us
know whether you're aware of any inaccuracies in the sequence of single
sub-clone regions. We are also interested in feedback from you to let
us know where you access our finished data. Do you look in EMBL at
individual finished clones, and therefore see the miscellaneous feature
tags in the EMBL header? Or do you wait until the sequence has been
annotated and access this from Vega? If you could let us know that
would give us an idea of how useful our miscellaneous feature tags are
to you. Please send your emails to pig-help@sanger.ac.uk by 20 March
2009. We look forward to hearing your opinions to help us generate
finished data as efficiently as possible while still providing as much
information as you need (kindly provided by Carol Churcher and
colleagues).
o o o o o o o o o o o
With the renewal of a new NRSP-8 project, members are encouraged to
provide input to the NRSP-8 Bioinformatics coordination team to help
identify the highest priority needs of the animal genome research
community. For those members that did not previously get a chance to
fill out a survey form at the Plant and Animal Genome meeting, the
bioinformatics team has placed the same survey on-line.
http://www.animalgenome.org/bioinfo/survey3.php . Please provide your
input by Monday March 3th. The Bioinformatics Team tries to provide at
no cost to the users tools/databases/computational resources that meet
their needs. To address the needs, that either go beyond the resources
provided to the Bioinformatics Team or are specific to a very small
group of users, some survey questions address the willingness to share
the expenses for the development or provision of such resources. Thank
you to all NRSP-8 members that have filled out the survey. Your input
is greatly appreciated. This information will help the coordination
team set priorities for the future of the project. We want to work
toward meeting the needs of the NRSP-8 member (kindly provided by
Zhi-Liang Hu and James Reecy).
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
A Banff Swine Genomics Workshop was held to further engage Canadian
scientists and industry personnel in collaborative projects and grant
development. A first draft discussion paper was prepared by Graham
Plastow as background from the meeting. Copies can be obtained from
Graham Plastow and any comments and suggestions would be appreciated.
Please feel free to provide comments directly to Graham as well. His
email address is Graham.Plastow@ales.ualberta.ca and phone number is
(780) 492-1496.
o o o o o o o o o o o
PAG XVII, January 10-14, 2009 was a great success. The swine workshop
and the swine sequencing workshop both had excellent presentations
including one on the usefulness of the new 60K SNP chip. 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
USDA Grant update. The 2008 Farm Bill authorized the creation of the
Agriculture and Food Research Initiative (AFRI), which replaces the
National Research Initiative (NRI). AFRI offers research, education,
extension project opportunities that focus on six key areas of
importance to agriculture, nutrition, food safety, environment, and
rural communities. CSREES released the AFRI program announcement on the
agency's Web site
http://www.csrees.usda.gov/funding/afri/pdfs/program_announcement.pdf
and on http://grants.gov/ . The program announcement provides an
overview of the legislation that created the AFRI program and describes
programs being offered in Fiscal Year 2009. The program descriptions
contain the program priorities, deadline dates, budget limitations, and
contact information. The program announcement does not contain all
information needed to submit an application. That information will be
contained in the AFRI Request for Applications (RFA). The AFRI RFA is
anticipated in January 2009. Important information regarding the Animal
Genome, Genetics, and Breeding Program: The program name for the Animal
Genome program has been changed to "Animal Genome, Genetics, and
Breeding" Letters of Intent are required for research priorities 1
through 4 and the letter of intent deadline is March 5, 2009. The
proposal deadline for research priorities 1 through 4 is May 14, 2009
(kindly provided by D. Hamernik and P. Burfening).
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)
Midwest ASAS, ADSA regional meetings. March 16-19 in Des Moines IA.
Details at http://adsa.asas.org/midwest/2009/
British Pig Breeders Roundtable in 2009 - April 27th- 29th , Kent , UK
for information please contact marie-anne.robertson@genesis-faraday.org
"Enabling protein value chains" - University of Alberta livestock
genomics conference, Edmonton, Alberta, 28th-30th April 2009, contact
Graham Plastow at Plastow@ualberta.ca .
Statistical Genetics of Livestock for the Post-Genomic Era, May 4-6,
2009. University of Wisconsin, Madison, WI. Additional information can
be found by contacting grosa@wisc.edu.
Systems Biology: Integrative, Comparative, and Multi-Scale Modeling: The
18th Annual Growth Factor and Signal Transduction Conference, June
11-14, 2009, Iowa State U., Ames, Iowa. See
http://www.bb.iastate.edu/~gfst/phomepg.html
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 96 can be sent to me by no later than April 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 |
+-----------------------------------+--------------------------------------
