TITLE:

PHYLOGENETIC APPROACH TO GENE ANNOTATION AND FUNCTION PREDICTION (No. 112)

DATE:

Friday, April 21st, 2006

TIME:

3:30 PM

LOCATION:

GMCS 214

SPEAKER:

Scott Kelley, Department of Biology, San Diego State University

ABSTRACT:

The purpose of our study was to develop a phylogenetic-based (tree-parsing) algorithm for automated gene function annotation. Computer-based functional annotations of molecular sequences (DNA and proteins) based on sequence similarity matching and pattern recognition have proven to be powerful tools in molecular biology. The BLAST algorithm, in particular, has been used to annotate literally millions of genes and has been incredibly successful at identifying the biological function of numerous sequences. However, similarity searching algorithms, by themselves, cannot distinguish orthologous sequences (related through common ancestry) from paralogous sequences (similarity due to an ancestral duplication event). Using an example with bacterial porin genes, we show how reliance on automated BLAST searches can lead to extreme confusion and extensive mis-annotation of bacterial sequences. Our phylogenetic analysis of class 1 porin genes found numerous instances of incorrectly annotated sequences. Interestingly, this problem was not always solved through comparative analysis of gene position in related bacterial genomes, and we found strong evidence of allele swapping. Not only was our phylogenetic analysis able to greatly improve the quality of functional annotations, but we also uncovered a new potential functional class of porin proteins. Based on our successful phylogenetic analysis of porin sequences, we have developed an algorithm for automated phylogenetic functional annotation of sequences. We show that this algorithm works extremely well for porin annotation and we demonstrate how it might be applied to functional annotation of other genes.

HOST:

Paul Paolini

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