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AnGenMap Archived Post

From  Mon Apr 21 16:27:52 2014
From: "Hu, Zhiliang [AN S]" <>
Postmaster: submission approved
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#2,
Date: Mon, 21 Apr 2014 16:27:52 -0500

What's new on the NAGRP animal genome web site (#2, 2014)

o Animal QTLdb updates:

  Announcing Release 23 of the Animal QTLdb. 1,873 new QTL/associations
  have been added to the database since the last release in January. The
  new QTL/association data added to the database: Cattle: 875; Pig: 635;
  Chicken: 363. This led to the current total QTL/association number in
  the database: 24,875 [Cattle: 9,180; Chicken: 4,282; Pig: 10,497;
  Sheep: 789; Rainbow trout: 127].

  The new release also includes several new items:

  (1) The Animal QTLdb has been improved to include pleiotropic
  QTL/association data. The pleiotropy data can be accessed through the data
  summary of a publication: go to the details of a publication (abstract),
  then click on "List QTL" link to view any available pleiotropy data.

  (2) Thanks to Brian Dalrymple, Sean McWilliam, and James Kijas of CSIRO
  for providing sheep STS marker mapping information; now we have sheep
  QTL/association data mapped to the sheep genome.

  (3) The Animal QTLdb has been improved to allow users to analyze QTL by
  their trait types (e.g., "feed intake" includes "average daily feed
  intake", "days on feed", "dry matter intake", and "residual feed intake").
  To use this feature, browse the trait hierarchy to find a trait of
  interest, and click on its "linkout" icon to go to "find all QTL on this
  trait type". This brings up a genome view of all chromosomes showing all
  mapped QTL in the genome. When there are more QTL on a chromosome than the
  available space can hold, a "more" link will show up, to bring you to that
  particular chromosome with a full view of all QTL of the trait type on that
  chromosome. Currently this function is implemented only in Cattle QTLdb.
  Stay tuned...

  (4) Frustrated by too many Animal QTLdb search options/tools to choose
  from? Now there is a "grand search" tool available to simplify the
  database-wide search for you. The searched results are linked to each
  specialized search tool for you to explore further. Find it on the top of
  each species page, as well as the "Search Tools" pages.

  (5) The Animal QTLdb map view has been improved to allow users to view QTL
  data of user's choice on a chromosome for alignment display. To do so,
  first come up with a list of QTL IDs from your data mining process, then
  copy all QTL IDs into the "Search" box on a QTLdb chromosome view, then
  click "go".

  (6) Search for Vertebrate Trait (VT) Ontology, Product Trait (PT) Ontology,
  and Clinical Measurement Ontology (CMO) terms within the Animal QTLdb has
  been made possible. Use the current search tool "Find if your trait has a
  QTL" or "Grand search" to start. On the results page, VT/PT/CMO are now
  shown where mapped. Note on this page there are new choices on the top
  search box to limit the search "In VT/PT/CMO traits" or "all". For example,
  when "In VT/PT/CMO traits" is checked, the results will be limited to, AND
  grouped by, VT/PT/CMO traits only. In addition, if any QTL for the trait
  exists in "other" species, it is also listed for exploration of the same
  trait into a different species. Another way to start the search is from
  respective VT/PT/CMO project home pages; by the heading "Utility: Animal
  QTLdb", click expansion arrow to open a search box.


o NAGRP Data Repository updates:

  (1) The NAGRP VCF File Repository (beta version) is open to the public to
  accept file deposits. This platform is designed for collaborative VCF file
  storage, handling, information abstraction, querying, and data re-use. See
  the copy of our poster at the 2014 PAG for details: VCF Miner: A Platform
  and Tools for Collaborative Information Mining from Next-Generation
  Sequence Variant Data

  (2) Several Ensembl functionally annotated SNP chip data sets have been
  made available via NAGRP Data Repository. These include Ensembl VEP
  annotated bovine high-density (770K) SNP data, bovine low-density (6K) SNP
  data, bovine 50K SNP chip data, chicken 600K SNP chip data, horse 50K SNP
  chip data, and pig 60K SNP chip data (thanks to James Koltes for forwarding
  the information).

  (3) Two annotation data sets in '.bed' format have been made available by
  Heather Holl and Samantha Brooks from Cornell University to share with the
  horse genomics community. The data sets are on a de novo assembly of three
  lamellar transcriptomes. Alignment was performed to EquCab2 using BLAT and
  repeats have been filtered.


o A user forum on AnimalGenome.ORG is under development:

  A user-driven questions and answers information exchange forum is under
  development. This forum is designed to collect commonly useful Q&A from
  the AnimalGenome.ORG Helpdesk as a general reference source for users to
  look for answers to similar questions asked before. One such example is a
  user-contributed FAQ item recently added to the Animal QTLdb FAQ list. The
  Q&A is about how to transfer QTL mapping information from a current genome
  build to older versions (thanks to user Shangang Jia for input).

  URL: (not available at this time but see Animal QTLdb FAQ list for the item
  mentioned here:

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. Please 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), email us at the address below, or
use our online Helpdesk, which will instantly relay your query for best
response (

NAGRP Bioinfo Team



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