Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

The Cattle EST Gene Family Database

Anand Venkatraman , Christine G. Elsik

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

We have created the Cattle EST Gene Family Database using the Ensembl human protein dataset as a framework to assemble, translate and annotate cattle expressed sequence tags (ESTs). We use an approach that combines protein-to-translated DNA similarity search, EST contig assembly and protein family classification. An advantage of our approach is that it allows us to identify human homologs of rapidly diverging bovine genes that might be missed using DNA-to-DNA comparison. The results of clustering ESTs and classifying them into protein families are web accessible and searchable in two ways: (1) Cattle EST Gene Family Database Search Page and (2) GBrowse Cattle EST Assembly Viewer. An exchange interface interlinks the results of the two search methods. The Cattle EST Gene Family Database can be searched by a human protein attribute identifier (Ensembl, Swiss-Prot/Trembl, RefSeq), Gene Ontology, Enzyme Commission number or a descriptive term. The database can also be searched by Cattle EST Genbank identifiers (GI number or Accession). The search output includes information about the human protein family and the related cattle EST members. The GBrowse Cattle EST Assembly Viewer displays the alignment of ESTs to an EST contig. These resources, which will be useful for annotating cattle ESTs, can be accessed at http://racerx00.tamu.edu.