Genomics / Proteomics
Barker, Michael S. , Dinh, Louie , Rieseberg, Loren H. .
Orthology assessment in EST data sets by whole genome guided phylogenies.
Identifying orthologs is a requisite step of evolutionary genomic analyses. The most commonly used algorithm for ortholog assessment is to assign reciprical BLAST hits (RBH) as orthologs. However, the RBH approach has difficulty assigning orthologs in genomes with significant amounts of gene duplication, and this problem is exacerbated when data sets are incomplete. Unfortunately, this is the case with most plant genome data. Plant genomes are renowned for their gene and genome duplications, and most genomic data sets are ESTs which do not likely contain all members of plant gene families. To overcome these confounding factors of orthology assessment in plant genomes, we developed a new ortholog pipeline using whole plant genome sequences to guide the phylogenies of EST sequences. This approach leverages all of the available information about plant gene family members to provide robust assessments of orthology from any genomic data set, including ESTs. Using EST data sets generated by the Compositae Genome Project, we compare the accuracy of the RBH method and our "phylolog" approach to orthology assignment.
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1 - Indiana University, Department of Biology, Jordan Hall, 1001 East Third Street, Bloomington, Indiana, 47405, USA
2 - University of British Columbia, Dept. of Botany, Vancouver, BC, V6T 1Z4, Canada
3 - University of British Columbia, Department of Botany, 3529-6270 University Blvd, Vancouver, BC, V6T 1Z4, Canada
Presentation Type: Poster:Posters for Topics
Location: Ball Room & Party Room/SUB
Date: Monday, July 28th, 2008
Time: 12:30 PM