Title :
Sequence alignment on the Cray MTA-2
Author :
Bokhari, Shahid H. ; Sauer, Jon R.
Author_Institution :
Dept. of Electr. Eng., Univ. of Eng. & Technol., Lahore, Pakistan
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.
Keywords :
DNA; biology computing; dynamic programming; multi-threading; performance evaluation; sequences; Cray MTA-2; DNA sequences; ENRI; Electronic Navigation Research Institute; Japan; Multithreaded Architecture-2; bioinformatic applications; dynamic programming; full/empty bits; perfect speedup; performance; sequence alignment; Bioinformatics; Computer architecture; DNA; Dynamic programming; Hardware; Navigation; Sequences; Silicon; Supercomputers; Yarn;
Conference_Titel :
Parallel and Distributed Processing Symposium, 2003. Proceedings. International
Print_ISBN :
0-7695-1926-1
DOI :
10.1109/IPDPS.2003.1213285
