Plant, Animal & Microbe Genomes X Conference Plant, Animal & Microbe Genomes X ConferenceJanuary 12-16, 2002
Town & Country Convention Center
San Diego, CA
Bioinformatics: Databases
Comparative genomics comprises the realm of looking across the genomes of multiple species to better understand patterns of gene conservation and divergence. One of the goals is to integrate data on gene across species, say from model organisms to economically important ones. Phylogenomics is a term that is being used increasingly to mean the application of comparative genomics in an explicitly phylogenetic context. Essentially this means fitting models of phylogeny at both the species and at the gene level to represent multi-species, genome-scale sets of sequence data. We are building a database and automated analysis system designed to organize gene-related sequences into such a model. Pair-wise comparison (BLAST) is used to group sequences into initial homology sets, or putative gene families. Specially written tree-alignment code is then used to validate or break apart these initial homology sets. Sequences within each validated gene family are aligned and subjected to various kinds of tree-building, with multiple resulting trees being stored for each family. This database of gene family trees is being used to address questions such as finding ancient genome duplications. This system should improve understanding of genome annotation by being able to view all homologs (orthologs and paralogs combined), each with associated functional data, in the context of a single tree. We have begun analyses of data-rich plant species represented by large EST sets (tomato, soybean, Medicago, Arabidopsis, rice) looking at both single-gene-tree and gene ensemble questions in relation to the species phylogeny.