Parallel Methods in Computational Genomics

Anantharaman Kalyanaraman, PhD candidate
Department of Electrical and Computer Engineering
Iowa State University
www.public.iastate.edu/~ananthk

Abstract

Computational genomics has evolved into a vibrant field over the past two decades. Questions that are of fundamental importance to genomic science are being addressed through the development of computationally effective solutions. Several of these biological discoveries are direct outcomes of analyzing biological sequence data. With the sequence repositories exponentially growing in their sizes, their analysis is becoming increasingly complex. Concurrent with these developments, supercomputing technologies have also advanced tremendously. However, their computing potential remains relatively untapped in computational genomics research. My research focuses on the design and development of parallel algorithms and software for analyzing large-scale sequence data. Of particular interest are problems with an impending need for scalable high-performance computing solutions. In this talk, I will describe a parallel clustering algorithm that we developed for the following two applications: (i) clustering Expressed Sequence Tags (ESTs) which are a type of DNA sequence data used in gene-related studies, and (ii) clustering genomic data for maize genome assembly. The novelty of our approach lies in its space and time efficiency and its capability to exploit the vast computing power and memory easily available through distributed memory parallel computers. This work has significantly enhanced the problem size reach while also drastically reducing the time to solution.

Candidate Bio

Ananth Kalyanaraman is a doctoral candidate in Computer Engineering at Iowa State University. He received his M.S. in Computer Science from Iowa State University in 2002, and B.E. in Computer Science and Engineering from Visvesvaraya National Institute of Technology, Nagpur, India in 1998. His research interests include bioinformatics and computational biology, parallel computing, and string algorithms. Ananth is a recipient of IBM and Pioneer Hi-Bred graduate research fellowships. Recently, two of his publications were recognized with best paper awards (in conferences IPDPS'06 and CSB'05). He is a member of ACM, IEEE, and SIAM. More information can be found at his homepage: http://www.public.iastate.edu/~ananthk