Friday, 11 January 2013 at 11:30am
Room 1400 Biomedical and Physical Sciences Bldg.
Refreshments at 11:15
Speaker: David A. Liberles, Department of Molecular Biology, University of Wyoming
Title: Computational Approaches for Linking Comparative Genomics to Biochemistry and Evolution
Abstract:
Standard bioinformatics pipelines for the comparative genomic data analysis of protein-encoding gene families typically
include steps like multiple sequence alignment, phylogenetic tree reconstruction, calculation of the ratio of rates of
nonsynonymous to synonymous nucleotide substitution (dN/dS), and gene tree-species tree reconciliation. Models for amino
acid substitution used in these processes assume that each site evolves independently according to average properties in the
absence of a protein structural or functional context. Models for duplicate gene retention assume that the process is
evolutionarily neutral and do not consider functional or mechanistic underpinnings. A model for duplicate gene retention
that would allow for mechanistic differentiation between nonfunctionalization, neofunctionalization, subfunctionalization,
and dosage balance based upon differences in expected time-dependent retention profiles is presented. Two characterizations
of amino acid substitution are also presented. One approach extends a population genetic model to inter-specific genomic
data and a second approach evaluates the effects of selection for protein folding and protein-protein interaction on
sequence evolution. These approaches reflect an in progress strategy for increasing biochemical and evolutionary realism in
bioinformatics.