Research Article

Sequence alignment on the Cray MTA-2†

  1. Shahid H. Bokhari1,*,
  2. Jon R. Sauer2

Article first published online: 6 JUL 2004

DOI: 10.1002/cpe.808

Issue

Concurrency and Computation: Practice and Experience

Concurrency and Computation: Practice and Experience

Special Issue: High Performance Computational Biology

Volume 16, Issue 9, pages 823–839, 10 August 2004

Additional Information

How to Cite

Bokhari, S. H. and Sauer, J. R. (2004), Sequence alignment on the Cray MTA-2. Concurrency and Computation: Practice and Experience, 16: 823–839. doi: 10.1002/cpe.808

Author Information

  1. 1

    Department of Electrical Engineering, University of Engineering & Technology, Lahore 54890, Pakistan

  2. 2

    Eagle Research & Development, 1898 S. Flatiron Court, Suite 128, Boulder, CO 80301, U.S.A.

*Department of Electrical Engineering, University of Engineering & Technology, Lahore 54890, Pakistan

  1. †

    Affectionately dedicated to the memory of Harry F. Jordan

Publication History

  1. Issue published online: 6 JUL 2004
  2. Article first published online: 6 JUL 2004
  3. Manuscript Accepted: 8 SEP 2003
  4. Manuscript Received: 18 JUN 2003

Funded by

  • National Institutes of Health. Grant Number: 21HG02167-01

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Keywords:

  • bioinformatics;
  • sequence alignment;
  • DNA;
  • exact match;
  • approximate matching;
  • dynamic programming;
  • multithreading;
  • full/empty bits;
  • parallel processing;
  • MTA-2

Abstract

Several variants of standard algorithms for DNA sequence alignment have been implemented on the Cray Multithreaded Architecture-2 (MTA-2). We describe the architecture of the MTA-2 and discuss how its hardware and software enable efficient implementation of parallel algorithms with little or no regard for issues of partitioning, mapping or scheduling. We describe how we ported variants of the naive algorithm for exact alignment and the dynamic programming algorithm for approximate alignment to the MTA-2 and provide detailed performance measurements. It is shown that, for the dynamic programming algorithm, the use of the MTA's ‘Full/Empty’ synchronization bits leads to almost perfect speedup for large problems on one to eight processors. These results illustrate the versatility of the MTA's architecture and demonstrate its potential for providing a high-productivity platform for parallel processing. Copyright © 2004 John Wiley & Sons, Ltd.

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