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© Oxford University Press

A fast, sensitive pattern-matching approach for protein sequences

K. Rohde 1 and P. Bork 1,2

1Max-Delbrueck-Centre for Molecular Medicine Robert-Roessle-Strasse 10, 0-1115 Berlin-Buch
2European Molecular Biology Laboratory, Biocomputing Group Meyerhofstrasse I, W-6900 Heidelberg, Germany

Pattern-matching algorithms are a powerful tool for finding similarities and relationships among the steadily growing amount of known protein sequences. We present a fast, sensitive pattern-matching algorithm that describes a pattern by its physico-chemical properties rather than by occurrence ofamino acids, using a fast, dynamic programming algorithm. Selected examples will demonstrate applications and advantages of our approach.

Received on April 14, 1992; accepted on July 31, 1992

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