Seminars and Events - Research Colloquia

Special Colloquia, Department of Statistics

Tuesday, January 16, 2001
4:30 PM in MATH 215

Professor Jun Xie
University of California, Los Angeles

will speak on

A Bayesian Insertion/Deletion Robust Algorithm for Protein Motif Searching via Entropy Filtering

Abstract

Bayesian models have been developed for finding ungapped motifs in multiple protein sequences (Liu, Neuwald and Lawrence 1995). In this article, we extend the model to allow for deletions and insertions in the motifs. Direct generalization of the ungapped algorithm, based on Gibbs sampling, proves unsuccessful because the configuration space has become much larger. To alleviate this difficulty, a two-stage procedure is introduced. At the first stage, we use a method called entropy filtering which gives a crude estimate of amino acid frequencies in the motif without the concern of deletion/insertion patterns. A Metropolis-Hastings algorithm is applied in conjunction with entropy filtered frequency estimates. This eventually leads to a good starting value for the second stage processing. At the second stage, we switch to another Metropolis-Hastings algorithm for optimizing the alignment scores. This time the deletion/insertion pattern is incorporated in the algorithm. When applied to a data set consisting of 19 protein sequences from the globin-like superfamily taken from SCOP (http://scop.mrc-lmb.cam.ac.uk/scop/), our procedure identifies the motif regions of B and C helices.

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