TAMU Bovine QTL db and viewer Dave Adelson

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 v 2 (gbrowse) 487 – Number of qtl anchored on BGA v 3 (gbrowse) 457 – Number of SNPs within calculated qtl on BGA v 3(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 v 3 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.