From zhu iastate.edu Mon Apr 23 11:41:59 2012
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,
2012)
Date: Mon, 23 Apr 2012 11:41:59 -0500
What's new on the NAGRP animal genome web site (#2, 2012)
O Announcing Release 17 of the Animal QTLdb. This release includes 1,616
new QTL added to the database -- Cattle: 713; Chicken: 426; Pig: 386;
Sheep: 45; Rainbow trout: 73. Thanks to Cari Park for her diligent
curation efforts. Several new features on the QTLdb public portal are
highlighted below:
(1) The QTL map location conversion (cM to bp) algorithms were updated
and applied to programs for QTL data downloads. This update eliminated
several minor data conversion bugs.
(2) Now users can search multiple QTL to customize targeted QTL traits
for alignments and meta-plots (previously, this option was initially
designed only for comparisons within one trait across different studies).
(3) QTL overview within a super-trait (e.g., all "Disease Susceptibility"
traits) is made possible within the QTLdb trait browse tracks [Hint:
look for "Find all QTL for this trait type" link when browsing QTL by
traits].
(4) QTL publication summary by super-trait (trait-type) can be easily
generated when browsing trait hierarchies [Hint: look for "Find all
publications on this trait type" link when browsing QTL by traits]
(5) Literature search within the QTLdb can now be better defined by
using structured phrases to better target search scopes by authors,
journals, or publication time windows, etc. [Hint: Do a publication
search on QTLdb, see more search options on the return page]
In addition, an extensive overhaul of the QTLdb curator tools has been
completed, which accommodates the new database structure changes and
enhances our ability to de-bug data, resulting in improved quality control
processes within the QTLdb.
URL: http://www.animalgenome.org/QTLdb/
O The NAGRP data sharing repository continues to be heavily used by the
community. The newly added data for sharing include:
- New cattle 770k HD SNP and 64k SNP chip annotations were shared by
James Koltes (jekoltesiastate.edu) from Iowa State University
(http://www.animalgenome.org/repository/cattle/).
- A multisites contigs and Unigenes data set was shared with the chicken
genome community by Qinghua Nie (nqinghuaiastate.edu) from Iowa State
University (http://www.animalgenome.org/repository/chicken/).
URL: http://www.animalgenome.org/repository/
O Pig genome data updates:
- The Ensembl annotations based on miRNA, misc_RNA, Mt_rRNA, Mt_tRNA,
protein_coding, pseudogene, retrotransposed rRNA, snoRNA, and snRNA
data (from Susan Fairley [sf7sanger.ac.uk]) have been aligned to
pig genome 10.2 within GBrowse.
URL: http://www.animalgenome.org/...i-bin/gbrowse/pig10/
- Pig Affy array elements (both 2005 and 2010 versions) have been mapped
to pig genome build 10.2 by BLAST. We encourage users to share new
custom data set mappings to the pig genome build.
URL: http://www.animalgenome.org/..._mappings/
- QTL for different pig trait types have been added as separate tracks
within GBrowse to improve the ability to visualize QTL data
URL: http://www.animalgenome.org/...i-bin/gbrowse/pig10/
O The Vertebrate Trait (VT) Ontology, a controlled vocabulary for the
description of vertebrate morphological, physiological, and developmental
traits (measurable or observable characteristics) is available for viewing
on AnimalGenome.ORG. This project is a collaborative effort between
Iowa State University, Mouse Genome Informatics, the Rat Genome Database,
and the French National Institute for Agricultural Research (INRA). VT terms
are annotated to QTL data in the Animal QTLdb to facilitate cross-species
comparisons of data. Along with the VT, the Product Trait Ontology (PT)
and Clinical Measurement Ontology (CMO) are also available online. Please
contact Cari Park (cariparkiastate.edu) for questions/suggestions.
URL: http://www.animalgenome.org/...bin/amico/browse.cgi (CMO)
http://www.animalgenome.org/...bin/amido/browse.cgi (PO)
http://www.animalgenome.org/...bin/amion/browse.cgi (VTO)
O Upon the successful completion of the virtual comparative mapping tool
development as a collaboration between Iowa State University, the University
of Iowa, and the Medical College of Wisconsin, the VCmap has been made
available on AnimalGenome.ORG. This tool uses a java "web start" to launch
the application on any computer platform. Currently, genomic and genetic
data from humans, mouse, rat, cattle, chicken, horse, and pigs are available.
More comparative data can be added when they become available. We also look
forward to your suggestions to make it more useful for you.
URL: http://www.animalgenome.org/VCmap/
O The CRI-MAP Improvement Consortium web site "downloads" area is
upgraded for users to upload and share their contributions. Interested
users can join this user forum to see their activities improve the
CRI-MAP, a project led by Dr. Jill Maddox from University of Melbourne.
URL: http://www.animalgenome.org/tools/share/crimap/
O A "SheepModels" listserv mailing list is set up for interested users to
discuss the use of sheep as biological research models and related
topics. Currently, there are 270+ users on the list. Please feel free
to join them if you are interested.
URL: http://www.animalgenome.org/...ommunity/SheepModels
If you need a mailing list for your community group, collaboration
project, or other needs, you are welcome to send us a request.
O NRSP-8 Aquagenomics, Pig genomics, and Bioinformatics Coordination
annual reports were posted. Check respective species web sites for
details. Archived reports are also available.
URL: http://www.animalgenome.org/
O Sheep genome web site has been modified to reflect the change of NAGRP
"Sheep" to "Sheep/Goat" Genome Coordination Program. A number of
other updates can also be seen on the web site.
URL: http://www.animalgenome.org/sheep/
As always, suggestions from the livestock community are welcome. We are
here to serve the community. Please forward your suggestions or comments on
how we can improve the existing services and tools, or what new services/
tools you need, by either calling Jim Reecy at +1-515-294-9269 or e-mailing
us 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. It would be appreciated
if you could kindly report to us any dead links, web site errors, or
mistakes whenever you come across them when browsing AnimalGenome.ORG
--
NAGRP Bioinfo Team
bioinfo-teamanimalgenome.org
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