Archived Post

From  Thu Jan 10 15:47:50 2008
Date: Thu, 10 Jan 2008 15:47:28 -0600
From: Zhiliang Hu <>
To: Multiple Recipients of <>
Subject: What's new on the NAGRP animal genome web site (#1,

What's new on the NAGRP animal genome web site:

- 1 -
A new linux cluster computer with 8 nodes, a total of 16 processors
is commissioned. We have installed the mpiblast, and developed web tools
to accept, queue blast jobs and send results to users. This is a great
boost to the blast capacity we have.

To make better use of its computing power for the community, we need
inputs from you on, (1) what sequence database we should build (besides
the genomes of human, cattle and chicken)?  (2) Any other applications
to utilize its parallel computing power?  Discussions on large scale
data analysis may also be useful.

- 2 -
The Animal QTLdb Release #6 -- A new release of Animal QTLdb is available.
Several things are new in this release: (1) the number of curated QTL for
cattle, chicken and pigs are 1,124, 657, and 1,675 respectively; (2) More
structural genomic information is aligned with respective QTL maps, which
include alignments of 18,183 SNPs, 14,728 affy-microarray elements, 15,627
oligo-microarray elements to the bovine genome, 4,528 new microsatellites,
435 gene-based SNPs, 18,487 affy-microarray elements, 16,700 oligo-
microarray elements to swine genome, and 2,978 SNPs to chicken genome.

- 3 -
Additional 838 porcine microsatellites with repeat motives of three to
six bases have been added to the Pig QTLdb for alignment. This is an
addition to the previously aligned 4,528 porcine microsatellite markers.
Thanks to Peter Karlskov-Mortensen and Merete Fredholm from the Royal
Veterinary and Agricultural Univ. of Denmark for providing the data.

- 4 -
Animal Trait Ontology Project web site was renovated, with additions
of (1) a user guideline for collaborators, (2) a discussion forum for
the project participants, (3) AmiGO browser to view the ATO hierarchy.
Thanks to Laron Hughes for some of the works he put in on this.

- 5 -
1.8 million cattle SNPs from Baylor are aligned to cattle QTL maps.
Thanks to George Weinstock of the Texas Medical Center for his kind
helps to obtain the new cattle SNP data.

- 6 -
A preliminary experiment to align and display microarray expression
data seems successful.  Thanks to Shu-hong Zhao from Huazhong University
for providing the testing data.

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

NAGRP Bioinfo Team



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