Archived Post

From  Tue Apr 28 10:54:59 2015
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 (#2,
Date: Tue, 28 Apr 2015 10:54:59 -0500

What's new on the NAGRP animal genome web site (#2, 2015)

o Animal QTLdb updates:

  Announcing Release 26 of the Animal QTLdb: A sum of 5,344 new QTL/
  associations have been added to the database--Cattle: 4,763; Chicken:
  146; Horse: 13; Pig: 412; Sheep: 10. The current total number of QTL/
  associations in the database: 37,409 (Breakdown: Cattle: 17,908; Chicken:
  4,525; Horse: 1,018; Pig: 13,030; Sheep: 801; Rainbow trout: 127).

  We thank volunteer curators for entering new data. We particularly
  appreciate the efforts of Nick Serao from Iowa State University and
  Tatsuhiko Goto from Hiroshima University. We encourage all authors of
  new QTL/association studies to get a curator account and directly enter
  their data into the database, to improve accuracy and share the curation

  A new data type, Signature of selection is being added to the database,
  please stay tuned...

  We have devoted the past few months to debugging/rebuilding the processes
  by which QTL/association map location data are converted to allow correct
  display in GBrowse/JBrowse.  We thank those who reported problems to us.
  Should you notice anything odd, please feel free to contact us.


o GenomeWeb interviewed Jim Reecy, the lead coordinator for NRSP-8
  Bioinformatics activities within the National Animal Genome Research
  Program: NAGRP Bioinformatics Arm Seeks Input from Livestock Genomics
  Community to Set Future Priorities.  A survey will be distributed to the
  community members soon.


o Support continues for OMIA -- the Online Mendelian Inheritance in Animals:
  Because the long-term sustainability of OMIA was becoming uncertain in
  Sydney, it was agreed in March 2015 that the OMIA master database would be
  moved to Iowa State University (ISU), where it will become part of the bioinformatics resource. A new site has been set up at
  ISU for hosting the OMIA master database. The transition from Australia
  to Iowa State will happen in the coming months. This is part of our efforts
  to facilitate collaborative further development of OMIA. The plan is to
  have a developmental/main site in the USA, and a mirror site in Australia.

  Relevant URLs:
   Current home:
    Future home:
   OMIA Support:

o The NAGRP Data Share Repository now has over 1000 files for sharing.
  To help users quickly locate files of interest, a new search function has
  been implemented on the data repository site.  With this tool, users can
  quickly narrow down the area for targeted files.


o A new web site has been set up for the international consortium on
  Functional Annotation of Animal Genomes (FAANG), which supports
  efforts among international scientists for collaborative activities.
  Interested users can find project description, project planning, recent
  publications, supporting and contributing member lists, and online
  wiki/forum for users. Registered users can find communication channels
  for several working committees and have access to archived documents.


o A new, improved version of CRI-MAP has been made available by Jill
  Maddox on the CRI-MAP Improvement web site. The main change in this
  version pertains to the implementation of a version of parallelization
  using forks and pipes for the get_likelihoods function. This means that
  flips, all, and build will use multiple CPUs when more than one order
  is being tested.


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
( which will relay
your query for prompt response.

NAGRP Bioinfo Team



© 2003-2024: USA · USDA · NRPSP8 · Program to Accelerate Animal Genomics Applications. Contact: Bioinformatics Team