From zhu iastate.edu Mon Jan 6 13:33:33 2014
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,
2014)
Date: Mon, 06 Jan 2014 13:33:33 -0600
What's new on the NAGRP animal genome web site (#1, 2014)
o Announcing Release 22 of the Animal QTLdb. 1,317 new QTL/associations
have been added to the database since the last release in August. The
current QTL/association number in the database: 23,002 [Cattle: 8,305;
Chicken: 3,919; Pig: 9,862; Sheep: 789; Rainbow trout: 127].
The new release also included several new items:
(1) Horse QTLdb: Many THANKS to Cecilia Penedo of UC-Davis, Andy Law of
Roslin Institute, Samantha Brooks of Cornell University, and Ernest
Bailey of University of Kentucky; now the Animal QTLdb has the structure
set up for collecting horse QTL/association data. Please note it will
take a while for the new horse data to pass curation and release
pipelines before they show up on the Horse QTLdb portal.
(2) New members to Animal QTLdb data alliances:
- Ensembl: Thanks to Fiona Cunningham, Animal QTLdb data is now
synchronized to Ensembl. To use, go to http://www.ensembl.org and choose
a species to search for a trait name; among the output results, all
QTL/association data are flagged by "Phenotype" in parentheses. You can
utilize all Ensembl tools to explore further on your traits of interest.
The genome features are linked back to Animal QTLdb for curated details.
- UCSC: Thanks to Pauline Fujita and Robert Kuhn, Animal QTLdb data is
now synchronized to the UCSC genome site. Users are expected to be able
to utilize the UCSC genome viewer and tools for trait variation
alignments/analysis. Work is still on the way. Stay tuned.
Please note that data at Ensembl or UCSC is for species that has a genome
assembly available (e.g., cattle, chicken, sheep, or pig).
(3) Animal QTLdb Search Tools are being reformatted for users to easily
locate information for exploration, or to easily find data access points
for analysis.
- NEW: QTL genome distribution query tool: New search tools have been
added to allow users to view genome location distributions of targeted
traits. Go to "Search" -> "Data Analysis Tools" -> "Find QTL genome
distributions on a particular trait" to try it out.
- NEW: User-defined download tool by genome locations: Users now can
search and download QTL data by user-defined genome locations (in terms
of "bp"). Go to "Search" -> "Data Analysis Tools" -> "Find QTL by their
genome locations", for species that have a genome build (currently
cattle, chicken, and pig).
(4) New data types in the Animal QTLdb: In parallel to the classical
"QTL" data, we have modified the database and tools to allow curation of
eQTL and GWAS (association) data; now we are modifying the database and
tools to allow curation of copy number variation (CNV) data into the
database. It is our goal to be inclusive on all types of trait mapping
features linking phenotypes to genotypes.
(5) Welcome new curators to the Animal QTLdb; we now have 65 active
curator accounts. As always, we encourage all interested persons to
register for a curator account to actively enter new data.
URL: http://www.animalgenome.org/QTLdb/
o NAGRP shared data repository updates:
(1) New SNP genotype analysis/process scripts from Guangtu Gao, et al. of
USDA-ARS-NCCCWA are added to the NAGRP Shared Software Repository.
(2) Newly published rainbow trout SNP data is available through NAGRP
repository of hosted Supplementary Data to Publications (publication by
Yniv Palti, Guangtu Gao, et al. submitted to Molecular Ecology Resources).
URL: http://www.animalgenome.org/repository/
o NAGRP-8 species/bioinformatics coordinators information has been updated
to reflect the renewed NAGRP coordination structure for the next 5 years.
Please let us know if you would like to request new items or changes on
each species page.
o We offer free web space for NRSP-8 species coordinators, NAGRP
laboratories, or projects. If you would like to request a new site for
your lab or project, please let us know. If you have technical savvy
to maintain a site, we will be happy to accommodate your needs as well.
URL: http://www.animalgenome.org/ for species coordinator sites
URL: http://www.animalgenome.org/bioinfo/services/ for sample projects
We always appreciate your input. Please send us your suggestions or
requests any time. Communications sent to any of our coordinators or to
the web site contact addresses will be quickly gathered for evaluation and
handled in a timely manner.
Check out the daily "what's new" (http://www.animalgenome.org/news/whatsnew)
items for up-to-date information on this site. Thank you for kindly
reporting broken links or web errors on the AnimalGenome.ORG site.
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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