Archived Post

From  Fri Sep 23 14:26:33 2011
From: "Hu, Zhiliang [AN S]" <>
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#3
Date: Fri, 23 Sep 2011 14:26:33 -0500

What's new on the NAGRP animal genome web site (#3 2011)

o Announcing Release 15 of the Animal QTLdb with 14,239 total QTL in
  the database: (Break down: Cattle QTL: 4,802; Chicken QTL: 2,451; Pig
  QTL: 6,347; Sheep QTL: 639.  New QTL added to the database since the
  Release 14: Cattle: 120; Pig: 3; Sheep: 185).

  *** QTL data submission to the Animal QTLdb is now required by several
  journals prior to the publication of your paper. We encourage you submit
  your QTL data directly to the database through the curator web portal
  ( to speed up your paper review.

o A good news for AnGenMap listserv users - the File Share Platform can
  now be used as an alternative to share non-plain-text files that are
  normally not allowed as email attachments on the AnGenMap listserv
  (e.g. .PDF, .doc, .xls, .ppt, .xlm, files etc.)

o SNPlotz: Horse 54k and 74k SNP chip data has been added to SNPlotz.
  This expands the capabilities of SNPlotz to now include 7 SNPchip
  Datasets in 3 species. If you would like additional functions added
  to this tool please contact us with your ideas.

o A new GBrowse application has been setup for the horse with NCBI gene
  annotation data. Currently the custom data tracks for the horse include
  54k/74k SNPs, 3k RH and 10k STS marker data.

  *** If there are Gbrowse custom tracks that you would like developed
  for any of the livestock species, please contact us. We would love to
  hear from you.

o An experimental pig genome database is under development. A number of
  new functions and utilities are under development.  If you have any
  new idea for a pig genome database to better serve your purpose,
  please feel free to send your suggestions, note "pig genome database"
  in the "subject:" line, to

o A local copy of the Biomart has been installed on AnimalGenome.ORG to
  serve the livestock research community. Currently, queries against the
  pigs, cattle, chicken and horse genomes are supported.  More species
  will be added upon the availability of the data.

o The Blast Extension Analysis Program (BEAP) has been modified to
  assist users for easier setup. See the updated manual for details.

o The NAGRP data repository has been expanded to host supplementary data
  for publications. If you are looking for an online host for additional
  data to your publication, feel free to contact us at

o The new pig genome assembly has been actively improved during the
  summer.  The most recent build 10.2 has been submitted to NCBI and is
  available for blast analysis on the NAGRP blast server

As always, suggestions from the livestock community are always welcome. We
are here to serve to community. You can either call Jim Reecy at +1-515-
294-9269 or send us a note at

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

NAGRP Bioinfo Team



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