AnGenMap

Archived Post

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
  http://www.animalgenome.org/QTLdb/app.html

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.
  URL: http://www.animalgenome.org/...i-bin/util/fileshare

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:
  http://www.animalgenome.org/cgi-bin/util/2gff

o Pig genome preliminary assembly 9.2 annotated with NCBI gene models
  is now in GBrowse aligned with QTL and SNP data.
  URL: http://www.animalgenome.org/...cgi-bin/gbrowse/ssc/

o Cattle UMD 3.1 assembly, along with the new annotation, is included
  to align with QTL and SNPs at the NAGRP GBrowse site.
  URL: http://www.animalgenome.org/...-bin/gbrowse/bovine/

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
  us (http://www.animalgenome.org/QTLdb/faq.html#23).

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
  http://www.animalgenome.org/catfish/cbarbel/
  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.
  URL: http://www.animalgenome.org/repository/

  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
site: http://www.animalgenome.org/news/whatsnew.html

--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org



 
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