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© Oxford University Press

Searching for distantly related protein sequences in large databases by parallel processing on a transputer machine

Gerhard Vogt and Patrick Argos

European Molecular Biology Laboratory Meyerhofstrasse I. Postfach 102209, D-6900 Heidelberg. FRG

AliMac is an implementation of a sensitive sequence alignment algorithm on a parallel computer. The method achieves reliable alignments for very distantly related sequences from a combined use of amino acid exchange weights and physicochemical characteristics. The algorithm is computing intensive and its usage on conventional computers is limited to a relatively small number of sequences. The parallel implementation uses a Macintosh Hex host computer and 21 transputers and achieves 22 times the speed of a VAX 8650 at a fraction of the cost. This paper describes the AliMac hardware and software and discusses problems and peculiarities of parallel implementations, especially with transputers. Finally, several popular sequence alignment algorithms are compared in their ability to detect distantly related sequences in searching large databases.

Received on May 27, 1991; accepted on July 9, 1991

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