Christine Elsik, assistant professor of Animal Sciences at Texas A&M and director of that university's Animal Bioinformatics and Computational Laboratory (http://racerx00.tamu.edu), will speak to the Seminar on April 8.

Title: Protein Clustering to Assemble Families of Homeomorphic Proteins

Presentation slides: [Powerpoint]

Abstract: With the capacity for genome projects to generate thousands of protein sequences per year, we need an effective automated method to group these sequences into families of proteins with identical domain organization (homeomorphic). Assembling families allows us to perform phylogenetic analysis to identify orthologs. Many proteins are modular, consisting of more than one structural domain. The combination of domains in a protein determines its function. Current protein clustering algorithms do not effectively separate multidomain proteins that share a common domain, but differ in overall domain organization. One reason for the difficulty is that we do not know the domain organization of many novel proteins, but rely merely on amino acid sequence similarity to classify proteins. I will compare hierarchical protein clustering algorithms and present a hidden Markov model for identifying protein domains using only sequence information.