As far as I can determine, Andrew Coulson (biochemist) and John
Collins (computer scientist) from Edinburgh University were the first
to use specialized hardware for DNA/protein sequence database
searching. They used the DAP (distributed array processor) which
comprises 4096 bit addressable processors in parallel. The DAP was
developed by the British armed forces for military purposes, but was
discarded. They use a rigorous Needleman-Wunsch dynamic programming
algorithm together with a variety of PAM matrices (Dayhoff ref.)
for protein database searching. No shortcuts or compromises are
needed as in the FASTA algorithm. In my opinion, their combination of
hardware and software is still the best.
Like Geir Hauge, I have heard many promises of specialized chips, but
I have not seen results.
Collins, J. F. and Coulson, A. F. W. (1984).
"Applications of parallel processing algorithms for DNA sequence
Nucleic Acids Res. 12, 181-192.
Coulson, A. F. W., Collins, J. F. and Lyall, A. (1987).
"Protein and nucleic acid sequence database searching: a suitable
case for parallel processing."
The Computer Journal 30, No. 5,420-424.
Dayhoff, M. O., Schwartz, R. M. and Orcutt, B. C. (1978).
"A Model of Evolutionary Change in Proteins." In Atlas of Protein
Sequence and Structure, Vol. 5, Suppl. 3, National Biomedical
Research Foundation, Washington, 345-352.
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