AnGenMap

Archived Post

From zhuiastate.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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