Sequence Alignment on the Cray MTA-2

Authors:
Shahid H. Bokhari;Jon R. Sauer
Affiliations:
-;-
Venue:
IPDPS '03 Proceedings of the 17th International Symposium on Parallel and Distributed Processing
Year:
2003

Citing 0
Cited 1

Parallel sequence alignment: a lookahead approach

PReMI'05 Proceedings of the First international conference on Pattern Recognition and Machine Intelligence

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Abstract

The standard algorithm for alignment of DNA sequences using dynamic programming has been implemented on the Cray MTA-2 (Multithreaded Architecture-2) at ENRI (Electronic Navigation Research Institute), Japan. Descriptions of several variants of this algorithm and their measured performance are provided. It is shown that the use of "Full/Empty" bits (a feature unique to the MTA) leads to implementations that provide almost perfect speedup for large problems on 1-8 processors. These results demonstrate the potential power of the MTA and emphasize its suitability for bioinformatic and dynamic programming applications.