Archived Post

From  Tue Sep 22 08:35:58 2009
From: Zhiliang Hu <>
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#3,
Date: Tue, 22 Sep 2009 08:35:58 -0500

What's new on NAGRP animal genome web site (#3, 2009)

o Announcing the Release 9 of the Animal QTLdb:
   Owing to diligent and hard work by our QTLdb Curator Cari Park,
   we are catching up with backlogs of literature to be curated.
   To date, a total of 4,079 new QTL have been added to the database
   (Cattle: 983; Chicken: 502; Pig: 2,594, including 897 eQTL).

o Virtual Comparative Map (VCMap):
   As a result of collaborations between Iowa State University,
   the Medical College of Wisconsin, and University of Iowa, we are
   happy to release a preliminary trial version of the Virtual
   Comparative Map (VCMap) tool (URL:
   Please feel free to try things out, and send any feedback to:
   URL: (see "NEW" link)

o Rainbow Trout Linkage map on-line:
   Thanks to Caird Rexroad and colleagues, we are able to make
   the rainbow trout 2nd generation genetic map available on-line:

o New computer server:
   The NAGRP Bioinformatics web sites and databases have been
   moved to a new computer server.  Although we try to make the
   site structure as consistent as possible, surprises may exist.
   We will appreciate your help to report any broken links, missing
   items, malfunctions, among other glitches, by email to

   The "old" computer server will be upgraded in terms of its OS,
   database engine and programming platforms, and will serve as
   a developmental portal for the community.

o SNPlotz:
   We have developed a genome plot tool for SNP association studies
   in collaboration with Dorian Garrick's group at the Iowa State
   University. This program is targeted to aid users for high-throughput
   SNP data analysis.  Initially, we designed the program to plot the
   "phenotypic effect" values associated with SNPs, with respect to their
   genome locations.  Users can then link out to Gbrowse to visualize SNP
   locations with respect to genome locations of known genes, curated QTL,
   etc.  We are in a process of modifying the program to make it more
   flexible in terms of how to define the input data in more generic terms.
   Please try it out and send us any feedbacks.

o NRSP-8 Bioinformatics Web Portal:
   The NAGRP Bioinformatics web site is undergoing preparation
   for a new face lift in order for the community to better access
   the tools and databases easily and readily.  We have attempted
   a few front pages, but please let us know your thoughts and input!
   More suggestions for improving the web site are always welcome.

o NRSP-8 Bioinformatics Services:
   We have developed an infrastructure and scheme to host bioinformatics
   web sites/contents and databases.  Several collaborative database
   development experiments are being carried out with several NRSP-8
   laboratories.  We encourage everyone you may wish to make
   use of this service to contact us for additional details.

Check out the "what's new" page for more up-to-date information on this

NAGRP Bioinfo Team



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