TAMU Bovine QTL db and viewer

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TAMU Bovine QTL db and viewer

• Dave Adelson
• Texas AM University

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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.

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Bovine QTL viewer
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QTL database
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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

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Beta testing

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

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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.

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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.

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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.