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AnGenMap Archived Post

From  Tue Sep  2 13:45:47 2014
From: "Hu, Zhiliang [AN S]" <>
Postmaster: submission approved by list moderator
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#3,
Date: Tue, 02 Sep 2014 13:45:47 -0500

What's new on the NAGRP animal genome web site (#3, 2014)

o Animal QTLdb updates:

  Announcing Release 24 of the Animal QTLdb: A sum of 3,876 new QTL have
  been added to the database since last release.  This brings the current
  total number of QTL in the database to 28,624 [Breakdown: Cattle: 11,543;
  Chicken: 4,337; Horse: 345; Pig: 11,610; Sheep: 789; Rainbow trout: 127].
  Thanks to Tatsuhiko Goto from Hiroshima University (Japan) for contributing
  data and his curation works.

  The new release also includes several new additions to the QTLdb:

  (1) The first horse QTL/association data are now publicly available. 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 for their helps during the Horse QTLdb setup.

  (2) Data alliances: The complete implementation of livestock animal QTL
      tracks at the UCSC site took extended time and they have finally been
      made available in the recent release of the UCSC Genome browser for
      cattle, chicken, pig, and sheep. Thanks to Pauline Fujita and Robert Kuhn
      for their diligent work to facilitate this.

  (3) A new QTLdb curator tool has been added to help users batch deposit their
      QTL/association data. As a matter of fact, among 3,876 newly curated QTL/
      association data, two thirds of them were curated using this tool.

  (4) A new search tool has been added to the Animal QTLdb to allow query of
      neighboring QTL/associations by a user-defined view window. Its utility
      comes with a sliding window, also defined by user on viewing size and
      slide distance. The tool also includes a graphical representation of the
      two window positions relative to their chromosome locations. Hyperlinks
      enable users to visualize alignments of the QTL/associations in GBrowse.

   Erratum: We thank Dr. Miri Cohen-Zinder from Isreal for her collaborative
            efforts in shaping this tool in its developmental stage.

  (5) We have begun to create video tutorials to introduce new tools developed
      for Animal QTLdb users to easily access and analyze the QTL data curated
      into the database. More tutorials are to be added in the coming weeks.
      We welcome users to contribute video tutorials to share their experiences
      regarding discovery of QTLdb utilities.


o Data repository:

  - Thanks to Jeremy Walker (, the pig 70K SNP chip
    annotations are now available from the NAGRP data repository.

  - A horse genotype VCF file is shared from Claire Wade (University of Sydney)
    and Jessica Petersen (University of Nebraska-Lincoln).

  - Genome updates: The latest releases of NCBI genome annotations for
    several livestock species have been updated through the NAGRP shared data
    repository (cattle: 2013-08-06; chicken: 2013-06-19; pig: 2013-09-29; horse:
    2013-09-23; Look for "Genome_annotations" sub-folder in respective species
    folders). Information is also linked from each NAGRP species home pages.


o Toolbox:

  - The CateGOrizer is now bundled with a new external tool, Revigo, for the
    convenience of users to take CateGOrizer outputs directly to Revigo for a
    semantic representative subset analysis.

  - VCmap: A video tutorial has been made available on workarounds to a VCmap
    Menu dysfunction on MacOS platform (contributed by James Koltes, Iowa State


Check out the daily "what's new" ( items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links or web errors on AnimalGenome.ORG.

Your input is always appreciated. Feel free to contact us any time with your
needs, requests, and/or suggestions. You can reach us in multiple ways:
contact Jim Reecy (+1-515-294-9269) for new projects/priorities, email the team
at the email address below, or use our online Helpdesk to get in touch with the
team ( which will relay
your query for prompt response.

NAGRP Bioinfo Team



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