Determination of optimal local sequence alignment similarity score

Sequence arrangement and sequence database similar retrieval are used for some purposes which are in the inside of a task [that it is the most important and challenging] in bio information science, and include protein function prediction. The efficient parallel processing of the sequence arrangement algorithm of the Smith * ウォターマン using parallel processing is shown in the form of SIMD (single instruction, multiple data) technology. Although it is mounting using MMX (multimedia extension) and SSE (streaming SIMD extension) technology which are embedded at the newest microprocessor of Intel, the method, However, the method can also be mounted using the same technology that exists in other newest microprocessors. Speedup of about 8 times is accepted about the optimized thing of the fastest attained until now [of eight kinds of parallel processing approaches] by mounting the Smith * ウォターマン un-in parallel with the same hardware. 500-MHz Intel Pentium with single speed called renewal of per second about 200 million cells It is obtained by the III (R) microprocessor.