From zhuiastate.edu Thu Aug 23 22:35:28 2012
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#3, 2012)
Date: Thu, 23 Aug 2012 22:35:28 -0500
What's new on the NAGRP animal genome web site (#3, 2012)
O Announcing Release 18 of the Animal QTLdb. This release includes 1,006
new QTL added to the database. Less obsolete ones, the new QTL by species:
Chicken - 280; Pig - 633; Sheep - 69; and Rainbow trout - 15. Credit goes
to Cari Park for her diligent curation efforts. Thanks are also due to
Sixin Liu from USDA National Center for Cool and Cold Water Aquaculture for
addition of a number of rainbow trout QTL. In addition, the functions of
the QTLdb continue to be improved, including obsolete QTL data withdrawal
from NCBI (THANKS to Wonhee Jang for his great assistance), and development
of a new procedure to update temporary literature IDs in the QTLdb curation
pipeline to avoid repeated data entry.
O Data archiving and sharing at the AnimalGenome.ORG site continues to undergo
improvement. Besides the community-wide free data download platform and
individualized private data transportation, authenticated data access is
among the new capabilities added to the data sharing platform. Our goal is
to work with community members for easier data archiving and retrieval,
simple or structured data sharing (i.e., on project, group, or other pre-
defined basis), and usage of other data tools, such as database-aided data
handling, to meet your needs.
O QTLdb: As the QTLdb curator/editor tools are improved, we encourage all
who have a curator account to use the tool to enter data, and encourage
all who are interested to register for an account (yes, all can be done
online via a web browser). The latest addition to the tool set is a
private mail listserv among all curators to receive notification when
new QTL publications are available.
O QTLdb: Search for animal breeds associated with QTLs is made possible.
Note that this new function is still in an experimental phase, with known
bugs and certain limitations. Please report any odd observations as you
see them. (go to "Search" sub-header under a species to use it).
O QTLdb: A new trait navigator is made available for users to browse the
trait hierarchy trees for their QTL (go to "Browse" sub-header under a
species to use it).
O We have been actively constructing an Animal Trait (Genetic) Correlation
database for some time. By developing this Database, our aims are to
collect all published livestock animal phenotypic/genetic trait
correlations study results, and develop tools to link such information
with QTL/association data. The ultimate purpose of this effort
include but not limited to facilitating genetic network and meta-
analysis among other potential applications. If you are interested
in this effort, and would like to get involved in terms of fine tuning
the design and/or data curations, we will be happy to hear from you.
O The pig genome build 10.2 annotations are ported to the BioMart setup at
the AnimalGenome.ORG site for customized downloads.
O Pig OligoArray elements are BLAST mapped to pig genome build 10.2 and
available for download.
O VCmap User's Manual is finally available online. The Virtual Comparative
Map tool was developed by our out-sourcing software company Bio::Neos and
is hosted at the AnimalGenome.ORG site. The manual goes with its latest
version (3.0). Let us know if you see anything not well addressed.
O For the approaching Plant and Animal Genome (PAG) conference, the room-
share database is now open upon request. Please take advantage of this
tool to share your hotel costs.
We are here to serve the livestock genomics community. Please forward your
suggestions or comments on how we can improve the services and tools, or
what new services/tools you need. Call Jim Reecy at +1-515-294-9269 or
e-mail us directly at bioinfo-teamanimalgenome.org
Check out the "what's new" page for more up-to-date information on this site
(http://www.animalgenome.org/news/whatsnew). Thank you for kindly reporting
any dead links, web errors, or mistakes on AnimalGenome.ORG.
NAGRP Bioinfo Team