SIMD solution to the sequence comparison problem on the MGAP

Manjit Borah, Raminder S. Bajwa, Sridhar Hannenhalli, Mary Jane Irwin

Research output: Contribution to journalConference article

26 Scopus citations


Molecular biologists frequently compare an unknown biosequence with a set of other known biosequences to find the sequence which is maximally similar with the hope that what is true of one sequence, either physically or functionally, could be true of its analogue. Even though efficient dynamic programming algorithms exist for the problem, when the size of the database is large, the time required is quite long even for moderate length sequences. In this paper we present an efficient pipelined SIMD solution to the sequence alignment problem on the Micro-Grain Array Processor: a fine-grained massively parallel array of processors with nearest neighbor connections. The algorithm compares K sequences of length O(M) with the actual sequence of length N in O(M + N + K) time with O(MN) processors which is AT-optimal. The implementation on the MGAP computes at the rate of about 0.1 million comparisons per second for sequences of length 128.

Original languageEnglish (US)
Pages (from-to)336-345
Number of pages10
JournalProceedings of the International Conference on Application Specific Array Processors
StatePublished - Dec 1 1994
EventProceedings of the 1994 International Conference on Application Specific Array Processors - San Francisco, CA, USA
Duration: Aug 22 1994Aug 24 1994


All Science Journal Classification (ASJC) codes

  • Hardware and Architecture
  • Computer Networks and Communications

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