From zhuiastate.edu Sat Apr 23 14:53:15 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 (#2, 2011)
Date: Sat, 23 Apr 2011 14:53:15 -0500
What's new on the NAGRP animal genome web site (#2, 2011)
o Announcing Release 14 of the Animal QTLdb:
This release includes several new features, functions and
newly curated data as hightlighted below:
(1) The Cattle QTL data has been aligned to UMD3.1 genome build (Thanks
to Steven Salzberg's group at University of Maryland for mapping STS
markers to make this possible). The data are available from both Gbrowse
(http://www.animalgenome.org/gbrowse/) and the Cattle QTLdb.
(2) The Sheep QTLdb is now linked to NCBI Entrez Gene database (Thanks
to Wonhee Jang of NCBI who developed a sheep genome template to make
such links possible). e.g. any QTL within the Sheep QTLdb can be linked
to NCBI Entrez Gene database.
(3) A new GBrowse track has been added to align Chicken 60K SNPs with
chicken genome/QTL/etc (Thanks to Martien Groenen of Wageningen
University for providing the Chicken 60K SNPchip mapping data).
(4) The QTLdb chromosomal viewer has been improved to allow users to
select from a list of traits for targeted QTL browsing. In addition,
the top tool bar has been improved to allow users to search for multiple
traits, and use wild cards (*) for partial non-specific matches. The
QTLdb FAQs have been updated to reflect these new features.
(5) As of April 20, 2011, there were 13,931 QTL in the database: 4,682
cattle QTL, 2,451 chicken QTL, 6,344 pig QTL, and 454 sheep QTL.
o The 2nd generation rainbow trout genetic map database has been updated
with 369 new markers and information updates on 1096 markers (updated
Feb 24, 2011).
o Catfish pseudo-chromosomes are available on GBrowse as part of cBARBEL,
which is being developed by John Liu's group at Auburn University.
o Numerous minor improvements/updates have been made to the tools
developed at and/or hosted by the NAGRP Bioinformatics Tool Box:
Improved to allow user's space for re-use of uploaded files for data
re-analysis with new configurations. The advantages are two folds: (a)
if you have a 30MB data file, you will need to upload the file only once
for multiple plot analyses; (b) if you have multiple phenotype columns
in a file, you can plot multiple times from the same uploaded file by
simply changing the configuration for each plot. Any user can register
for an account to manage your own data files. Click "User Login" for
(2) The 4.1 million Cattle dbSNP(rs) are now available in SNPlotz.
(3) The Expeditor Tool has been modified modified to fit newly updated
Ensembl gene structure formats.
(4) The File Share Platform:
Integrated user profile management with AnGenMap (continued efforts are
being made to overcome timeout issues with very large files).
(5) The CateGOrizer tool has been updated to allow users access to
intermediate data in order to better analyze the output. (b) Automation
of GO data updates have been implemented.
o Two new links have been added to the AnimalGenome.ORG web site (please
see the lower portion on the front page): (1) a web form for users to
better reach the Helpdesk; (2) a hierarchy list of the major web
resources on the site to serve as a Road Map for users to easily find
items of their interests.
Your support is vital for the AnimalGenome.ORG web sites and databases to
better serve the research community. We would like to ask all community
members to continue your support by forwarding your suggestions/comments
on how we can improve our services and tools, what new services/tools do
you need, and what can benefit the community as a whole. Feel free to
contact Jim Reecy (email@example.com or bioinfo-teamanimalgenome.org),
any of the species coordinators and/or bioinformatics co-coordinators for
your inputs (http://www.animalgenome.org/.../team.html).
Check out the "what's new" page for more up-to-date information on this
NAGRP Bioinfo Team