Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

Phylogenomic Analysis Of Animal And Plant Genomes

Kimmen Sjolander

  University of California, Department of Bioengineering, 473 Evans Hall #1762, Berkeley, CA 94720

Protein families evolve a multiplicity of functions and structures through gene duplication, domain shuffling, speciation and other processes. As numerous studies have shown, function prediction by homology is associated with systematic errors on these data. Phylogenomic analysis--combining phylogenetic tree construction, integration of experimental data, and differentiation of orthologs and paralogs--has been shown to address these errors and improve the accuracy of functional classification. The explicit integration of structure prediction and analysis in this framework, which we call structural phylogenomics, provides additional insights into protein superfamily evolution.
The Berkeley Phylogenomics Group is developing Animal proteome and Plant proteome phylogenomic resources for the scientific community. These phylogenomic HMM libraries enable classification of proteins to functional subfamilies, prediction of protein structure, family and subfamily specificity positions, and cellular localization.
In this talk, I will present new methods developed by my group for key tasks in a phylogenomic pipeline, and results of these analyses on selected protein families.