From zhuiastate.edu Wed Jan 2 12:23:44 2013
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 (#1, 2013)
Date: Wed, 02 Jan 2013 12:23:44 -0600
What's new on the NAGRP animal genome web site (#1, 2013)
o Announcing Release 19 of the Animal QTLdb. This release includes addition
of 1,249 new QTL (384 pig and 864 cattle QTL). In addition, more data
fields have been added to the Animal QTLdb data download files (e.g.,
"test models", "significance levels", and "map types"), so that users can
sort them for their own analysis.
A paper on recent developments of the Animal QTLdb has been published in
Nucleic Acids Research (2013, volume 41 (D1): D871-D879). This paper
summarizes all new developments on the QTLdb in the past few years.
o Announcing a preliminary release of the Animal Trait Correlation Database
(CorrDB). The purpose of the CorrDB is to house all livestock animal trait
correlation and heritability data published to date, in order to facilitate
future genetic network analysis. Currently the database has an initial
collection of 3,635 cattle correlation data on 276 traits.
A poster on the developments of the CorrDB will be presented at the coming
Plant and Animal Genome (PAG) conference in San Diego (Poster #P0960).
o The site to host supplementary data to publications for NAGRP members
continues to be actively used. Recent additions to supplementary data
include "Genome-wide association study implicates testis-sperm specific
FKBP6 as a susceptibility locus for impaired acrosome reaction in
stallions" by Raudsepp et al., and "Genome-wide analysis reveals selection
for important traits in domestic horse breeds" by Petersen et al.
o Thanks to James Koltes a series of VCMap Video Tutorials are available
online via youtube.com. The available topics include:
- Accessing VCMap
- Comparing 2 Maps Across Species
- Comparing Different Map Types and New Maps
- Exploring Detailed Homology and Gene Information
- Adding Annotation Information
- Using the Ontology Filter
- Loading Custom Annotations
- Exporting Images to File
- Creating Map-based Annotation Reports on Syntenic Regions Across Species
- Comparing QTL with Ontology Information
o As the sheep genome assembly 3.1 data became available recently, we tried
to complement the data sources for new sheep genome data to facilitate
community data analysis. The NAGRP served data include: the assembled
sequences in fasta format by chromosomes, corresponding gff files for
download, the same data served on NAGRP blast server, and alignments to
sheep BACs and 50k SNPs on GBrowse.
o In collaboration with Dr. Frank Nicholas of The University of Sydney, gene
alignments in OMIA are added as new GBrowse tracks for cattle, chicken,
horse, and pigs. Efforts are still on the way to keep it improved.
o A newly improved version of CRI-MAP software is available from Jill Maddox.
o Thanks to Martien Groenen of Wageningen University the dbSNP "rs" and "ss"
numbers for the pig 60K SNPs are now available on the NAGRP Data Repository.
We are here to serve the livestock genomics community. Please forward your
suggestions or comments on how we can improve and what new services/tools you
need. Call (Jim Reecy +1-515-294-9269) or email (bioinfo-teamanimalgenome.org)
to get in touch.
Check out the "what's new" (http://www.animalgenome.org/news/whatsnew) for more
up-to-date information on this site. Thank you for kindly reporting brocken links
or web errors on AnimalGenome.ORG.
NAGRP Bioinfo Team