From zhuiastate.edu Tue Jan 11 10:17:04 2011
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1, 2011)
Date: Tue, 11 Jan 2011 10:17:04 -0600
What's new on the NAGRP animal genome web site (#1, 2011)
o Announcing Release 13 of the Animal QTLdb:
As of December 31, 2010, a total of 1,190 new QTL have been added to
the database. This included 401 for cattle, 167 for chicken, 358 for
pigs, and 264 new QTL for sheep (http://www.animalgenome.org/QTLdb/)
o Migration of Sheep QTLdb from its Australia site to Iowa State
University is complete. The Sheep QTLdb was set up by Jill Maddox
at the University of Melbourne (Australia) in 2007 using the software
developed by Hu et al. at ISU (http://sphinx.vet.unimelb.edu.au/QTLdb/).
While the Australia site may have ceased accepting new data, new sheep
QTL data contributors are encouraged to apply for a curator account at
o File Share Platform: A data sharing space on the NAGRP server is created
for members to share data files with colleagues, collaborators or with
the entire community. AnGenMap members only need to have access to a fast
internet connection for file upload via a web browser in order to use it.
o New SNP data types have been added to the GFF Data Formatter tool. If
you have a subset of SNP names from Bovine 54k, 60k or Swine 50k chips
and wish to view them on GBrowse, this is the right tool for you:
o Pig genome preliminary assembly 9.2 annotated with NCBI gene models
is now in GBrowse aligned with QTL and SNP data.
o Cattle UMD 3.1 assembly, along with the new annotation, is included
to align with QTL and SNPs at the NAGRP GBrowse site.
o A preliminary QTL meta-analysis tool is added to the QTLdb. This
meta-analysis is based on cumulative QTL incidences along a chromosome
when QTL browse/search has resulted in a single trait. There are
two types of meta-analysis plots: a pile plot and a kernel density plot.
A manuscript is in preparation, and further improvement is underway.
If you are interested in sharing your ideas and requests, please contact
o Cytogenetic G-banded chromosome ideograms have been added to QTL maps
within the QTLdb for cattle, sheep, pigs and chicken. We thank Andy Law
of Roslin Institute for providing the G-band coordinates data. The new
chromosome ideograms will help facilitate user mining of QTL data
with reference to the cytogenetic chromosome locations. See the
QTLdb FAQ for details: http://www.animalgenome.org/QTLdb/faq.html#16
o Catfish Genome Database - Catfish Breeder and Researcher Bioinformatics
Entry Location web site (cBARBEL) is now online. For details, please
see recent paper by Lu et al. that appears in the January Database issue
of Nucleic Acids Research. The site can be seen at
or at http://www.catfishgenome.org/cbarbel/
o A web site for the Ruminant Genome Biology Consortium activities is now
online. It is hosted at the NAGRP Bioinformatics site and can be seen at
either http://www.animalgenome.org/...ruminants/ or http://www.ruminants.org/
o A data repository has been set up by the NRSP-8 Bioinformatics Team for
the research community to share data. Currently available data sets are
for cattle and pigs contributed by those who are acknowledged on the site.
For those who wish to share data with the community, please contact your
species or bioinformatics coordinators, or directly contact the NAGRP
Bioinformatics Team (bioinfo-teamanimalgenome.org), or use the NAGRP
File Share Platform described above.
Check out the "what's new" page for more up-to-date information on this
NAGRP Bioinfo Team