Biological sequence alignment on the computational grid using the GrADS framework

In spite of the existence of several Grid middleware projects, developing and executing programs on the computational Grid remains a user intensive process. The Grid Application Development Software (GrADS) project is working to make the Grid easy to use despite the dynamically changing status of Grid resources. Several software packages are being ported to the GrADS framework in order to guide its development. In this paper, we present the work done to Grid-enable a biological sequence alignment package (FastA) and to run it under the GrADS framework. Protein and genome sequence alignment is a basic operation in bioinformatics and tends to be very compute intensive. We discuss the advantages of using GrADS framework for FastA.