From listmasteranimalgenome.org Fri Apr 28 09:24:19 2017
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
Postmaster: submission approved by list moderator
To: Members of AnGenMap <angenmapanimalgenome.org>
Subject: What's new on the NAGRP animal genome web site (#2, 2017)
Date: Fri, 28 Apr 2017 09:24:19 -0500
What's new on the NAGRP animal genome web site (#2, 2017)
o Animal QTLdb updates:
Announcing Release 32 of the Animal QTLdb. A sum of 4,498 new QTL
have been added to the database. The current total number of QTL in
the database: 125,753 [Breakdown: Cattle: 98,090; Catfish: 0; Chicken:
6,791; Horse: 1,275; Pig: 17,955; Sheep: 1,515; Rainbow trout: 127]
(New additions less obsolete/retracted ones: Catfish: 0; Cattle: 2,758;
Chicken: 158; Horse: 30; Pig: 1,449; Sheep: 103; Rainbow trout: 0 -- Net
QTL number increase: 4,498).
(1) Access to the Wordle representation of QTL/association-mapped traits
by year, across all species, can now be found in the data summary area of
each species on the Animal QTLdb.
(2) Efforts have continued to improve QTLdb curator/editor/release tools
and procedures in terms of debugging (both data and tools), adding new
parameters, and optimizing the procedures for various data updates,
especially to meet the challenges of accommodating multiple genomes,
aligning map coordinates between linkage maps, SNP-represented coordinates,
manually entered coordinates, and coordinates conversions where needed.
o New Pig Genome Assembly version 11.1:
A new pig genome assembly build, version 11.1, submitted to NCBI by a
research team headed by Dr. Alan Archibald at the Roslin Institute, is
installed on the NAGRP Blast server for blast searches. The assembly is
available for both blastn and megablast searches.
Annotations to this build are not currently available, but are expected
to be added in the coming months. Stay tuned.
NCBI and Ensembl are the major public data sources/tools for animal
genomics research, and they both have evolved relatively quickly in recent
years. In order to help users more efficiently use their sites, we have
set up new web pages for their tutorials and workshop recordings arranged
so that users can easily find the guides they need.
o NAGRP Toolbox:
(1) The SNP 'rs' numbers assigned by NCBI dbSNP are not always instantly
available when the SNPs are used for a study; however, it's important to
match them up for post-experiment data analysis, meta-analysis, and other
purposes. A tool to batch match Illumina SNP names, custom SNP names, and
custom-assigned initial IDs to their respective dbSNP 'rs' numbers was
developed and has been made available through a web interface. The cattle
data were provided by Robert Schnabel, and pig data were provided by
Martien Groenen et al.
(2) New meeting information continues to be added to the meeting
information bulletin board. We encourage community members to contribute
new meeting information to the site.
o Data repository:
(1) A new camel data repository has been added upon request from Heather
Holl of University of Florida. We expect new data to be deposited soon.
(2) The repository for supplementary data to publications continues to
facilitate publication of papers with additional data depositions. We have
helped Animal Genetics journal to publish three (3) papers since January.
o FAANG web site update:
The FAANG web site has been updated with new funding opportunities and
funded projects information. Since its inception over 2 years ago,
FAANG consortium membership has grown to 321 contributors, 27
supporters, and 109 subscribers from 387 institutions in 49 countries.
Currently, there have been over 10 grants awarded to 28 researchers in
25 institutions. New input and ideas are always welcome to foster for
more positive actions.
Efforts are being made to establish a secured web connection for the
FAANG web site (similar to https://www.animalgenome.org). Stay tuned
for upcoming notifications.
o Web server:
We have enabled the AnimalGenome.ORG website to use Secure Sockets Layer
(SSL) connections, requiring the use of HTTPS protocol which is available
in almost all modern web browsers. Please make your future visits to:
The new secure connection encrypts all web traffic on this website. This
helps to protect your privacy and makes the site more resistant to cyber
We plan to completely switch to the HTTPS service by July 1, 2017. Before
that date, both regular (http://www.animalgenome.org) and secure services
will be available. However, we encourage you to switch to using the new
secure connection for future visits and to update your bookmarks and web
links during this grace period.
o Upcoming web sites update:
We develop and host web sites for a number of animal genomics/genetics
- https://www.animalgenome.org/pig/ (pig genomics)
- https://www.animalgenome.org/cattle/ (cattle genomics)
- https://www.animalgenome.org/sheep/ (sheep genomics)
- https://www.animalgenome.org/poultry/ (poultry genomics)
- https://www.animalgenome.org/bioinfo/ (bioinformatics)
Most of them were initially drafted over 10 years ago. While animal
genomics research has progressed rapidly, some of the content/links of
these web pages are becoming outdated. They need to be updated in order
to keep up with the community’s needs for an information hub.
We request your input, in terms of ideas for new layout, better
organization to meet new content demands, and removal of outdated
links/content. Please send your input to bioinfo-teamanimalgenome.org,
or each species may wish to combine suggestions within the community for
more effective and desired changes.
Check out the daily "what's new" (https://www.animalgenome.org/news/) items
for more up-to-date information on this site. Thanks in advance for kindly
reporting broken links or web errors on AnimalGenome.ORG. Feel free to
contact us at 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 address given below, or use our
online Helpdesk web form
NAGRP Bioinfo Team