Implementation of Genetic Sequence Alignment Programs on Supercomputers

Authors:
Alexander Ropelewski;Hugh Nicholas;David Deerfield
Affiliations:
Biomedical Supercomputing Initiative, Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213, ropelews@psc.edu;Biomedical Supercomputing Initiative, Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213 nicholas@psc.edu;Biomedical Supercomputing Initiative, Pittsburgh Supercomputing Center, 4400 Fifth Avenue, Pittsburgh, PA 15213 deerfiel@psc.edu
Venue:
The Journal of Supercomputing - Special issue on supercomputing in medicine
Year:
1997

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Abstract

We have implemented exhaustive genetic sequence alignment codes on avariety of high performance computers. In this article, we compare andcontrast the implementation issues encountered on different highperformance computer architecture and the approaches used to overcomethese problems. In addition, we discuss advanced sequence alignmenttechniques, including context sensitive and multiple sequencealignments.