From zhuiastate.edu Tue Jan 6 13:39:42 2015
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Multiple Recipients of <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#1, 2015)
Date: Tue, 06 Jan 2015 13:39:42 -0600
What's new on the NAGRP animal genome web site (#1, 2015)
o Animal QTLdb updates:
Announcing Release 25 of the Animal QTLdb: A sum of 3,314 new QTL have been
added to the database. The current total number of QTL in the database:
32,065 [Break down: Cattle: 13,145; Chicken: 4,379; Horse: 1,005; Pig:
12,618; Sheep: 791; Rainbow trout: 127] (New additions less obsolete ones:
Cattle: 1602; Chicken: 42; Horse: 660; Pig: 1008; Sheep: 2).
(1) A state of the art online alignment tool, Jbrowse, has been setup for
QTL/association data alignment with annotated genes along with other genome
features. The advantage of Jbrowse is that it easily allows user quantitative
data - XYPlot, Density, in BAM or VCF format - to be loaded directly to a
user's browser for comparisons in the local environment. The links to JBrowse
can be found on the front pages of both AnimalGenome.ORG and Animal QTLdb.
(2) A preliminary application programming interface (API) has been added to
the Animal QTLdb. This implementation uses REST web service architecture
and XML markup language for structured data transmission in an unambiguous
manner. The added scriptable access to the QTLdb is intended to facilitate
a more dynamic access of QTLdb data for end users.
(3) Horse QTL data is now streamed to UCSC Genome Browser and Ensembl
database for alignment display and data mining using the tools available at
UCSC/ Ensembl; QTL data stream to NCBI is on the way.
(4) A Wordle representation of QTL/ Association discovery trends over the
years has been made as a fun project.
o Data repository:
The NAGRP VCF Data Repository is actively used. The most recent additions
are eight (8) VCF files from Drs. Ottmar Distl, Joern Wrede (Institute of
Animal Breeding and Genetics, Hannover), Dr. Ludovic Orlando (University of
Copenhagen, Centre for GeoGenetics), and Dr. Danika Bannasch (University of
California Davis). Thanks to Dr. Carrie Finno from University of California-
Davis for helps facilitating this.
o Community support:
A dedicated virtual machine platform is setup to develop cyber resources
for the Striped Bass Genome Database activity, a project led by Benjamin
Reading and Charles Opperman at North Carolina State University.
Check out permanent additions and daily updates on this site at
We appreciate any input reporting broken links or web errors, as well as
utility requests/ideas to improve the service to the community at the
NAGRP Bioinfo Team