NRSP-8 Bioinformatics/Database Update # 3

March 1, 2006

Query the Bovine SNP Database

Bioinformatics utility tool box

Animal Genomics Software Archive

What is new with USDA grants in Washington, DC

New projects

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: http://www.animalgenome.org/bioinfo/resources/util/q_bovsnp.html

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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: http://www.animalgenome.org/bioinfo/resources/util/

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Animal Genomics Software Archive. We have set up an animal genomics software archive site for publicly shared software (http://www.animalgenome.org/bioinfo/tools/share/ ). 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.

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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 . 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.)

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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:

March 05 - March 10, 2006 Event: Biology: Integrating Biology, Technology, and Computation Location: Taos, NM, USA Web: http://www.keystonesymposia.org/Meetings/ViewMeetings.cfm?MeetingID=789 April 02 - April 05, 2006 Event: 10th Annual International Conference on Research in Computational Molecular Biology (RECOM) Location: Venice, Italy Web: http://recomb06.dei.unipd.it/
May 16 - May 19, 2006 Event: 2nd International Symposium on Animal Functional Genomics Location: Henry Center, Michigan State University, East Lansing, MI Web: http://www.isafg.msu.edu/
May 24 - May 28, 2006 Event: Genomes, Evolution, & Bioinformatics (GEB2006) Location: Arizona State University, Tempe, Arizona Web: http://www.smbe.org/geb/
June 15 - June 18, 2006 Event: 7th International Conference on Bioinformatics 2006 (BIOINFORMATICS 2006) Location: Uhus, Denmark Web: http://www.birc.au.dk/bioinformatics2006/
August 04 - August 05, 2006 Event: The 6th annual Bioinformatics Open Source Conference (BOSC 2005) Location: Fortaleza, Brasil Web: http://www.open-bio.org/bosc2005/
August 06 - August 10, 2006 Event: Intelligent Systems for Molecular Biology (ISMB) Location: Fortaleza, Brazil Web: http://ismb2006.cbi.cnptia.embrapa.br/
August 13 - August 18, 2006 Event: 8th World Congress on Genetics Applied to Livestock Production Location: Belo Horizonte, MG, Brazil Web: http://www.wcgalp8.org.br/paginaInicial.do
August 20 - August 25, 2006 Event: 30th International Conference on Animal Genetics (ISAG 2006) Location: Porto Seguro, Bahia State, Brazil Web: http://www.cbra.org.br/eventos/XXXisag.do
August 30 - September 03, 2006 Event: 28th Annual International Conference of the IEEE Engineering in Medicine and Biology Society Location: Marriott Hotel at Times Square, New York, NY Web: http://embc2006.njit.edu
September 04 - September 08, 2006 Event: 4th International Workshop on Biological Data Management - BIDM 06 Location: Krakow, Poland Web: http://embc2006.njit.edu/
September 10 - October 13, 2006 Event: 4th European Conference on Computational Biology (ECCB/05) Location: Eilat, Isreal Web: http://www.eccb06.org/
September 13 - September 17, 2006 Event: Genome Informatics Location: Hinxton, UK Web: http://meetings.cshl.edu/meetings/infouk06.shtml
September 28 - September 29, 2006 Event: Computational Intelligence in Bioinformatics and Computational Biology Location: San Diego, California Web: http://eldar.mathstat.uoguelph.ca/dashlock/CIBCB2006/
October 16 - October 18, 2006 Event: IEEE Symposium on Bioinformatics and Bioengineering (BIBE) Location: Washington D.C Web: http://birg.cs.wright.edu/bibe06/
November 08 - November 14, 2006 Event: COMPUTATIONAL & COMPARATIVE GENOMICS Location: Cold Spring Harbor Laboratory, NY Web: http://meetings.cshl.edu/courses/c-ecg06.shtml
November 11 - November 15, 2006 Event: Biomedical and Health Informatics Location: Hilton Wahington & Towers, Wahington, DC Web: http://embc2006.njit.edu/

                    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
sponsored by the USDA/CSREES NRSP-8

http://www.animalgenome.org/
Mailing list: angenmap@animalgenome.org