University of Houston
Department of Computer Science

In partial fulfillment of the Requirements for the Degree of
Master of Science

LeelaPrasad Talanki
will defend his thesis

IPS Estimator- A Tool for Estimating the Intensity of Purifying Selection in Protein-Coding Genes

Abstract
Functional constraint on protein-coding genes can be estimated by comparing the rates of evolution of genes and their paralogous pseudogenes. Studying the purifying selection on a group of monophyletic organisms can be helpful in inferring the taxon-specific rate of mutation and rate of evolution. One approach for estimation utilizes a set of three aligned sequences: a processed pseudogene from a species, its conspecific paralogous gene, and an orthologous functional gene in another species. With these sequences one can estimate the number of substitutions along the branches that lead to the pseudogene(KΨ) and to the functional gene(Kg). The ratio of Kg and KΨ is used to estimate the fraction of mutations that are subject to purifying selection.

An application has been developed to estimate the intensity of purifying selection in orthologous protein-coding genes from two organisms using a multi-step process. Firstly, the best paralogous pseudogene for every gene in each organism is found. For each of these paralogous pairs, orthologs are next identified using a reciprocal BLAST approach. Additional filters have been included in the software application to verify the homology. Using sequence alignment, the distances can be calculated and thus the intensity of purifying selection. Herein, an example is provided for the computation of the intensity of purifying selection for protein-coding genes in human and mouse.

Date: 12 May, 2006
Time: 10:30 AM
Place: 550-PGH

Faculty, students, and the general public are invited.
Thesis Advisor: Dr. Yuriy Fofanov