NRSP-8 Bioinformatics/Database Update # 3

March 1, 2006

  1. Query the Bovine SNP Database
  2. Bioinformatics utility tool box
  3. Animal Genomics Software Archive
  4. What is new with USDA grants in Washington, DC
  5. New projects
  6. Upcoming meetings

Query the Bovine SNP Database. A database is set up using most recent bovine SNP released by Baylor. This database contains 114,958 bovine SNPs derived from multi-breed genome sequence information comparisons. A web interface is set up for public users to blast against the SNP flanking sequences and query the database for SNP details if good hits are found. URL:


Bioinformatics utility tool box. A bioinformatics utility tool box is set up at the NAGRP Bioinformatics site. Currently there are 6 utility tools in the "box": 1. Expeditor: Design primers gene structure and EST information from different species. 2. Prim2: Design primers on the consensus of 2 similar sequences. 3. A sequence alignment diagram drawing tool. 4. Gene ontology (GO) terms classifications counter. 5. DNA Sequence Reverse Complement Converter 6. Query the Bovine SNP Database by blast. URL:


Animal Genomics Software Archive. We have set up an animal genomics software archive site for publicly shared software ( ). Those who wish to share their software with the community, please feel free to contact us for information on how to deposit your software to this archive.


What is new with USDA grants in Washington, DC. The new USDA-NRI request for applications is available. You can access it at . We want to remind everyone that 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.)


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.




                    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


NAGRP Bioinformatics Coordination Program
sponsored by the USDA/CSREES NRSP-8
Mailing list:

© NAGRP Bioinformatics Coordination Program