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Sequence alignment on the Cray MTA-2

By: Bokhari, S.H.; Sauer, J.R.;

2003 / IEEE / 0-7695-1926-1


This item was taken from the IEEE Conference ' 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.