Archived Post

From  Thu Jan  5 09:49:45 2012
From: "Hu, Zhiliang [AN S]" <>
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#1,
Date: Thu, 05 Jan 2012 09:49:45 -0600

What's new on the NAGRP animal genome web site (#1, 2012)

o Announcing Release 16 of the Animal QTLdb. This release includes several
  new features, functions and newly curated data.  Some highlights are listed
  below (see our PAGXX poster #2566 for more details):

  (1) ATO/QTL traits are now mapped to Vertebrate Trait Ontology (VT),
  Product Trait Ontology (PT) and Clinical Measurement Ontology (CMO) (see
  our PAGXX poster #4054 for details) to help standardize the trait
  nomenclature used in the QTLdb. One can see these changes when they browse
  individual traits. For example:

  (2) The QTLdb has been revamped to accommodate genome map (map unit: bp)
  based QTL and association data (e.g. GWAS data). The map view and QTL
  details view have been updated to integrate these new data types.  A new
  user option allows one to view "QTL", "eQTL", "associations", or
  combinations of these data. For example:

  (3) Animal breed information can now be obtained for QTLs. While this data
  has been subject to curation for a few years, it can now be seen on the QTL
  detail page.

  (4) New function added: now lists of references are available for all QTL
  seen within a chromosomal view a user query/browse to.

  (5) Rainbow trout was added as a new member of species in the Animal QTLdb
  thanks to efforts by Yniv Palti and Caird Rexroad, III from the USDA
  National Center for Cool and Cold Water Aquaculture.

  (6) With the addition of 802 new QTL (pig: 85, cattle: 405, chicken:
  285 and rainbow trout: 27), the QTLdb now contains 15,014 QTL (also include
  association/GWAS data).  A big thanks goes out to Yoo Chae-Kyoung, who
  contributed 87 swine QTL.  By using the QTLdb curator tools, he was able
  to take advantage of the QTLdb option to keep his data in private for
  comparison with previously curated data prior to publication.

  The Animal QTLdb is now open to additions of new species, new QTL and
  association data.  Feel free to make use of it.  Here is your start point:

o New information on cattle 770K IllLumina High Density SNPs data:
  (1) "rs/ss" dbSNP ID matches, posted by Robert Schnabel.
  (2) Structural genomics analysis data, posted by James Reecy.

o The new pig genome database has been under active development. A number
  of new functions and data resources have been integrated.  It's close
  to being ready for a release.  See our PAGXX poster #3839 for details.

o AUGUSTUS pig gene predictions by Henrik Hornshoj et al were ported to
  GBrowse for data alignment.  New data will continue to be added as they
  become available.

o The Biomart installed on the AnimalGenome.ORG server has been serving the
  community well.  The most recent new data addition include the UMD 3.1
  bovine genome build annotated by Ensembl.

o New GBrowse tracks for 8.4 million cattle SNPs and 3 million chicken SNPs
  from dbSNP have been added as new tracks to respective Gbrowse setup.

o New items added in AnGenMap FAQ:
  (1) How to write effective emails on AnGenMap?
  (2) What can be posted on AnGenMap?
  We strongly encourage *new users*, especially the first time posters,
  to take a look at the FAQ. Since we now have 2000+ members on the AnGenMap
  list serve, proper use of the listserv is a concern for all.

o Our online Helpdesk ( has been
  functioning well in terms of both providing helps to users and obtaining
  user feedback to foster new ideas.  We thank all users who have contributed

Suggestions from the livestock community are always welcome. Your support
is vital to help improving the AnimalGenome.ORG databases and tools to
better serve the community. Please forwarding your suggestions/comments to, OR contact Jim Reecy ( or
any of the NRSP-8 species coordinators or bioinformatics co-coordinators
( to better prioritize
your requests.

Check out the "what's new" page for more up-to-date information on this

NAGRP Bioinfo Team



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