Plant, Animal & Microbe Genomes X Conference

January 12-16, 2002
Town & Country Convention Center
San Diego, CA

Bioinformatics: Databases
             

AN INTEGRATED GENOMICS DATABASE FOR BEEF CATTLE

¹ Department of Animal Science, Texas A&M University, College Station, TX 77843-2471

² Department of Biochemistry, Texas A&M University, College Station, TX 77843-2128

A data management system has been developed to maintain pre-existing genotypic and phenotypic data, as well as newly generated DNA sequences. Data from the Texas A&M Angleton project, resulting from the generation of reciprocal backcross families between Angus and Brahman cattle, have been assembled in a relational database. The database contains entries for 712 individuals, 84 phenotypes and genotypes for 406 markers. Web-based queries provide input for various statistical and mapping packages. Our continuing efforts to positionally clone genes affecting carcass and growth traits have resulted in the generation of several large sequence data sets (>5000 traces). Due to the recent limit in the size of batch jobs that can be submitted to NCBI for sequence similarity searches, we have implemented a local BLAST and FASTA pipeline on a 48CPU SGI Origin 3800 supercomputer. A collection of PERL scripts ports the ABI traces from a LINUX machine through the Phred/Phrap suite of programs to assign quality scores and remove any vector or E. coli sequences. Cleaned sequences are sent to Repeat Masker and then submitted to the supercomputer for similarity searches against appropriate databases. Many of our sequences come from BACs and similarity searches against the assembled human genome thereby provide comparative positional information on these BACs. Parsed BLAST output is then added to our relational database. Since we are constantly generating new sequence data and the public databases continue to expand, our BLAST results are refreshed on a weekly basis.