Biological sequence alignment on the computational grid using the GrADS framework

Asim Yarkhan; Jack J. Dongarra

doi:10.1016/j.future.2005.02.002

Biological sequence alignment on the computational grid using the GrADS framework

Asim Yarkhan, Jack J. Dongarra

Computer Science and Mathematics Div

Research output: Contribution to journal › Article › peer-review

17 Scopus citations

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.

Original language	English
Pages (from-to)	980-986
Number of pages	7
Journal	Future Generation Computer Systems
Volume	21
Issue number	6
DOIs	https://doi.org/10.1016/j.future.2005.02.002
State	Published - Jun 2005

Funding

This work was supported in part by the National Science Foundation contract grant #E81-9975020, SC R36505-29200099, R011030-09, “Next Generation Software: Grid Application Development Software (GrADS)”, and National Science Foundation contract grant #R38143-79200003, “GrADS Extension” and also in part by the Applied Mathematical Sciences Research Program of the Office of Mathematical, Information, and Computational Sciences, U.S. Department of Energy under contract DE-AC05-00OR22725 with UT-Battelle, LLC.

Funders	Funder number
National Science Foundation	38143-79200003, R011030-09, 81-9975020, SC R36505-29200099
U.S. Department of Energy	DE-AC05-00OR22725

Keywords

Biological sequence alignment
GrADS project
Grid scheduling

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10.1016/j.future.2005.02.002

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Biological sequence alignment on the computational grid using the GrADS framework

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Keywords

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