Biological sequence alignment on the computational grid using the GrADS framework

Authors:
Asim YarKhan;Jack J. Dongarra
Affiliations:
Computer Science Department, University of Tennessee, Knoxville, TN;Computer Science Department, University of Tennessee, Knoxville, TN and Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN
Venue:
Future Generation Computer Systems - Special section: Complex problem-solving environments for grid computing
Year:
2005

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Abstract

In spite of the existence of several grid middleware projects, developing and executing programs on the computational grid remains a user intensive process. The goal of the Grid Application Development Software (GrADS) project is to make the grid simpler to use despite the dynamically changing status of grid resources. Protein and genome sequence alignment is a basic operation in bioinformatics, and it requires large data sets and tends to be highly compute intensive. In this paper, we present work done to grid-enable a biological sequence alignment package (FASTA) and to run it under the GrADS framework. We discuss the advantages of using GrADS framework for FASTA.