AnGenMap Archived Post

From zhuiastate.edu  Mon Jan  6 13:33:33 2014
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1,
Date: Mon, 06 Jan 2014 13:33:33 -0600
What's new on the NAGRP animal genome web site (#1, 2014)

o Announcing Release 22 of the Animal QTLdb. 1,317 new QTL/associations
  have been added to the database since the last release in August. The
  current QTL/association number in the database: 23,002 [Cattle: 8,305;
  Chicken: 3,919; Pig: 9,862; Sheep: 789; Rainbow trout: 127].

  The new release also included several new items:

  (1) Horse QTLdb: 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; now the Animal QTLdb has the structure
  set up for collecting horse QTL/association data.  Please note it will
  take a while for the new horse data to pass curation and release
  pipelines before they show up on the Horse QTLdb portal.

  (2) New members to Animal QTLdb data alliances:
  - Ensembl: Thanks to Fiona Cunningham, Animal QTLdb data is now
  synchronized to Ensembl. To use, go to http://www.ensembl.org and choose
  a species to search for a trait name; among the output results, all
  QTL/association data are flagged by "Phenotype" in parentheses. You can
  utilize all Ensembl tools to explore further on your traits of interest.
  The genome features are linked back to Animal QTLdb for curated details.

  - UCSC: Thanks to Pauline Fujita and Robert Kuhn, Animal QTLdb data is
  now synchronized to the UCSC genome site. Users are expected to be able
  to utilize the UCSC genome viewer and tools for trait variation
  alignments/analysis. Work is still on the way. Stay tuned.

  Please note that data at Ensembl or UCSC is for species that has a genome
  assembly available (e.g., cattle, chicken, sheep, or pig).

  (3) Animal QTLdb Search Tools are being reformatted for users to easily
  locate information for exploration, or to easily find data access points
  for analysis.

  - NEW: QTL genome distribution query tool: New search tools have been
  added to allow users to view genome location distributions of targeted
  traits. Go to "Search" -> "Data Analysis Tools" -> "Find QTL genome
  distributions on a particular trait" to try it out.

  - NEW: User-defined download tool by genome locations: Users now can
  search and download QTL data by user-defined genome locations (in terms
  of "bp"). Go to "Search" -> "Data Analysis Tools" -> "Find QTL by their
  genome locations", for species that have a genome build (currently
  cattle, chicken, and pig).

  (4) New data types in the Animal QTLdb: In parallel to the classical
  "QTL" data, we have modified the database and tools to allow curation of
  eQTL and GWAS (association) data; now we are modifying the database and
  tools to allow curation of copy number variation (CNV) data into the
  database. It is our goal to be inclusive on all types of trait mapping
  features linking phenotypes to genotypes.

  (5) Welcome new curators to the Animal QTLdb; we now have 65 active
  curator accounts.  As always, we encourage all interested persons to
  register for a curator account to actively enter new data.

  URL: http://www.animalgenome.org/QTLdb/

o NAGRP shared data repository updates:

  (1) New SNP genotype analysis/process scripts from Guangtu Gao, et al. of
  USDA-ARS-NCCCWA are added to the NAGRP Shared Software Repository.

  (2) Newly published rainbow trout SNP data is available through NAGRP
  repository of hosted Supplementary Data to Publications (publication by
  Yniv Palti, Guangtu Gao, et al. submitted to Molecular Ecology Resources).

  URL: http://www.animalgenome.org/repository/

o NAGRP-8 species/bioinformatics coordinators information has been updated
  to reflect the renewed NAGRP coordination structure for the next 5 years.
  Please let us know if you would like to request new items or changes on
  each species page.

o We offer free web space for NRSP-8 species coordinators, NAGRP
  laboratories, or projects. If you would like to request a new site for
  your lab or project, please let us know. If you have technical savvy
  to maintain a site, we will be happy to accommodate your needs as well.

  URL: http://www.animalgenome.org/ for species coordinator sites
  URL: http://www.animalgenome.org/bioinfo/services/ for sample projects

We always appreciate your input. Please send us your suggestions or
requests any time. Communications sent to any of our coordinators or to
the web site contact addresses will be quickly gathered for evaluation and
handled in a timely manner.

Check out the daily "what's new" (http://www.animalgenome.org/news/whatsnew)
items for up-to-date information on this site. Thank you for kindly
reporting broken links or web errors on the AnimalGenome.ORG site.

NAGRP Bioinfo Team



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