论文信息 - Sequence alignment on the Cray MTA-2

Sequence alignment on the Cray MTA-2

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.

Shahid H. Bokhari | Jon R. Sauer

[1] Allan Porterfield,et al. Exploiting heterogeneous parallelism on a multithreaded multiprocessor , 1992, ICS '92.

[2] Shahid H. Bokhari,et al. Parallelizing a DNA simulation code for the Cray MTA-2 , 2002, Proceedings. IEEE Computer Society Bioinformatics Conference.

[3] Dan Gusfield,et al. Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[4] Simon Levin. Computational Molecular Biology An Introduction , 2000 .

[5] Allan Porterfield,et al. The Tera computer system , 1990, ICS '90.