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.

• Type: Conference
• Year: 2003
• Where: IPPS
• Authors: Shahid H. Bokhari, Jon R. Sauer
• Keywords: Distributed And Parallel Computing, Dynamic Programming, Dynamic Programming Applications, Electronic Navigation Research, IPPS 2003