NRSP-8 Bioinformatics/Database Update # 2
November 1, 2005 |
Development of Genetic/Genomics Software Database. In collaboration with
Dr. Wentian Li, North Shore LIJ Research Institute, we have developed a
database of more than 330 programs designed to analyze genetic/genomic
data (
http://www.animalgenome.org/soft ). To improve the ease of finding
available software, the database was designed so that it can be queried
by keywords or browsed alphabetically. Please contact Zhiliang Hu
(z...@iastate.edu) with any suggested improvements or additional data to
add to the database.
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What is new with USDA grants in Washington, DC. The new USDA-NRI
request for applications is available. You can access it at
http://www.csrees.usda.gov/funding/rfas/nri_rfa.html . This year there
is a specific call for bioinformatics proposals.
The Bioinformatics program requests applications for the
development of bioinformatic tools that will assist in functional
genomics, annotation and comparative genomics of agriculturally
important animals. These tools need to be designed to integrate with
existing data/databases (not create new ones), serve as tools for genome
analysis, provide for practical applications of genomic data and have a
biological framework.
FY 2006 Priorities for Research
1) Tools that integrate genome sequence, genome annotations and pedigree
information with biological function and phenotypic information for a
single species or across multiple species; and
2) Animal bioinformatics tools to efficiently and effectively handle
and interpret the genomic/ genetic data being generated to accelerate
the knowledge discovery process. (Examples include technology platforms,
computational resources and analytical tools for integrative and
comparative research.)
The total amount of support available for the Bioinformatics program
element will be approximately $1.5 million. The program element plans to
make 1 or 2 awards of up to $1 million each (including indirect costs)
for up to 4 years in duration.
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The Online Mendelian Inheritance in Animals (OMIA) has been revamped and
upgraded. The main change has been to move the master database to a MySQL
platform at the Australian National Genomic Information Service (ANGIS).
The results are: 1) a new web page (
http://omia.angis.org.au ) that
dynamically queries the master database; 2) access to abstracts (and
sometimes full papers) for papers with a pubmed ID; 3) far greater
possibilities for reciprocal linking with other web sites and 4) on-line
curation, which will enable input from colleagues with specialist
knowledge; and which, in time, will give OMIA a life beyond that of its
creator, Frank Nicholas. Another important development is that at the
request of NCBI, OMIA has been integrated into NCBI?s Entrez search
interface at
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIA . This
has given several new dimensions to OMIA, providing enhancements that
are not available from the ANGIS site. The content of the NCBI version
will be updated with regular dumps from the master database. These
developments have been achieved through the sterling efforts of many
people (see
http://omia.angis.org.au/acknowledgements.html ). The new
master database is still in its infancy. Input from interested
colleagues to make OMIA continually better is encouraged. The efforts
of Frank Nicholas are greatly appreciated (Kindly provided by Dr.
Rothschild).
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Generation of Comparative Maps. A graphic mapping presentation tool has
been developed to generate comparative RH-linkage maps on the fly
(
http://www.animalgenome.org/cattle/maps/RHMap3/). The tool has been
used for the online presentation of the data set from the recently
published cattle RH maps (SIAG-SUNbRH maps, Itoh et al., Genomics,
85(4):413-24). We plan to develop the tool further to facilitate
comparative mapping efforts.
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Mouse Genome Informatics (MGI,
http://www.informatics.jax.org/ ) is
pleased to announce the release of Version 3.3 of the database. Version
3.3 integrates the data on mouse models of human disease and human
disease etiology from OMIM with existing data for mouse genes and
strains in MGI. This enhances the exploration of phenotypes, sequence,
expression, orthology, and other related data. You can now use three of
the MGI query forms (Phenotypes and Alleles, Genes and Markers, Mouse
Sequence) to search for existing or potential mouse models of a
particular human disease and all human diseases that a particular mouse
(genotype plus strain background) can be used to model. Version 3.3
also incorporates data on mouse models sought without success, such as
models free from particular confounding diseases or phenotypic traits.
The database now links to Online Mendelian Inheritance in Man (OMIM)
descriptions of human diseases, syndromes, and conditions. The updated
query forms are for Phenotypes and Alleles is:
http://www.informatics.jax.org/searches/allele_form.shtml , for Genes and
Markers:
http://www.informatics.jax.org/searches/marker_form.shtml ; for
Mouse Sequence:
http://www.informatics.jax.org/searches/sequence_form.shtml and Human
Disease Vocabulary Browser:
http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=omimVocab&subset=A
(kindly provided by David Shaw)
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Update on the Pig QTL database. The pig quantitative trait loci (QTL)
database (PigQTLdb) (
http://www.animalgenome.org/QTLdb/ ) has been
recently published
http://dx.doi.org/10.1007/s00335-005-0060-9 . On
average about 11,000 web hits per month have been made to PigQTLdb in
the last few months. Several hundreds of new QTL data have been added
to the database. Stay tuned for next release soon. Please contact
Zhiliang Hu (z...@iastate.edu) with
any suggested improvements or
additional data to add to the database. We are currently also working
with the Aquaculture community to expand the utility of this resource.
In addition, we are working to incorporate the RH map and BAC end
sequence information as well.
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The livestock sequence Blast server. A NAGRP Blast Server is
now in service (
http://www.animalgenome.org/blast/ ). This blast server uses a
local copy of NCBI blast suite, which includes bl2seq, blastall,
megablast, blastpgp, blastclust, netblast, etc. The local sequence data
sets include all non-human, non-mouse EST sequences from the Genbank,
Whole Genome Shotgun (WGS) sequence assemblies for different organisms
from Genbank. These data sets are updated from Genbank every night.
The local sequence data sets also include TIGR Gene Indices for Cattle,
Chicken, Pig, Salmon, Catfish, and Rainbow Trout. The TIGR Indices are
updated weekly (done every Saturday night). Currently users can use the
web server for their blast. Links to the blast server are included on
each of the species pages under resources.
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New projects: As always if you have suggestions about what needs to be
developed/improved or how we can help please do not hesitate to contact
us. Jre...@iastate.edu
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UPCOMING BIOINFORMATICS MEETINGS
November 9-12, 2005. 8th Annual Conference on Computational Genomics
. Location: Cambridge, Massachusetts, USA
Web:
http://www.jax.org/courses/events/coursedetails.do?id=137
November 14-15, 2005. Computational Intelligence in Bioinformatics and
Computational Biology
. Location: San Diego, CA, USA
Web:
http://ieee-cis.org/cibcb2005/
December 8-11, 2005. 1st International Biocurator Meeting
. Location: Pacific Grove, CA, USA
Web:
http://tesuque.stanford.edu/biocurator.org//intnlbiocurator.html
January 3-7, 2006. PSB 2006 - Pacific Symposium on Biocomputing
. Location: Hawaii, USA
Web:
http://psb.stanford.edu/
January 21-25 2006. Lan Automation 2006
. Location: Palm Springs, CA, USA
Web:
http://labautomation.org/LA/LA06/
March 5-10, 2006. Systems Biology: Integrating Biology, Technology, and
Computation
. Location: Taos, NM, USA
Web:
http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=789
April 2-5, 2006. 10th Annual International Conference on Research in
Computational Molecular Biology
. Location: Venice, Italy
Web:
http://recomb06.dei.unipd.it/
April 3-7, 2006. ICDE 2006 - International Conference on Data
Engineering
. Location: Atlanta, GA,USA
Web:
http://icde06.cc.gatech.edu/index.html
June 6-8, 2006. International Conference On Computing & Informatics
. Location: Kuala Lumpur, Malaysia
Web:
http://www.conferencealerts.com/seeconf.mv?q=ca1a03h3
April 12-15, 2006. International Conference on Database Systems for
Advanced Applications
. Location: Hilton Hotel, Singapore
Web:
http://www.comp.nus.edu.sg/~dasfaa06/
June 15-18, 2006. The 8th international bioinformatics meeting
. Location: Aarhus, Denmark
Web:
http://www.birc.au.dk/bioinformatics2006/
July 2-7, 2006. Information Processing and Management of Uncertainty in
Knowledge-Based Systems
. Location: Paris, France
Web:
http://ipmu2006.lip6.fr/
August 6-10, 2006. The 14th Annual International conference on
Intelligent Systems for Molecular Biology. . . Location: Fortaleza, Brazil
Web:
http://ismb_2006.cbi.cnptia.embrapa.br/
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Items for the next update can be sent to me by no later than December 15
please.
James Reecy
U.S. Database/Bioinformatics Coordinator
2255 Kildee Hall
Department of Animal Science
Iowa State University
Ames, Iowa 50011-3150
Phone: 515-294-9269
Fax: 515-294-2401
Jre...@iastate.edu
http://www.animalgenome.org
© NAGRP Bioinformatics Coordination Program