TAMU Bovine QTL db and viewer

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TAMU Bovine QTL db and viewer Dave Adelson Texas A&M University

Bovineqtl.tamu.edu Provide a database of publicly available QTL in cattle. Front end for the database is a viewer that displays genomic context. Link to genome sequence and annotation.

Bovine QTL viewer

QTL database

Current limitations Assembly quality is the biggest problem. About 40% of STS defining QTL cannot be positioned on chromosomes. Total number of QTL in the bovine QTL viewer: 843 Number of qtl anchored on BGA v2 (gbrowse) 487 Number of qtl anchored on BGA v3 (gbrowse) 457 Number of SNPs within calculated qtl on BGA v3(gbrowse) : 575

Beta testing Search tool to find genes from QTL viewer using smart string/text matches. Automated literature search tool and interface for curation.

Bovinegenome.org Founding PIs: Christine Elsik, David Adelson and Mark Fahrenkrug. Model organism database for cattle. Will provide a one stop shop for cattle researchers. Will integrate data to provide features not available at NCBI, UCSC or Ensembl.

Bovinegenome.org Integration of QTL viewer with bovine EST resources and protein families. Addition of SNP/haplotype database and integration with genome browser and QTL viewer. Waiting for the SNP coordinates on assembly v3 at present. Only ~1500 available at present.

Thoughts for data formats and interoperability. Require authors to provide QTL data to a database upon acceptance by a journal. Details of significance of association for each marker tested should be required. Most data will now be SNP based rather than microsat based. Since each db will be curated differently, they should be interoperable via web services rather than mirrored.