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© 1988 IRL Press Ltd

Profile scanning for three-dimensional structural patterns in protein sequences

Michael Gribskov , Michelle Homyak , Jeffrey Edenfield and David Eisenberg

Molecular Biology Institute 405 Hilgard Avenue University of California Los Angeles, CA 90024-1570, USA

Profile analysis measures the similarity between a target sequence and a group of aligned sequences (the probe). The probe sequences are used to produce a position-specific scoring table (the profile) that can be aligned with any sequence (the target) using standard dynamic programming methods. We are developing a library of profiles, each describing a different structural motif. This allows any target sequence to be rapidly scanned for the presence of structural motifs. Levels of significance for the comparison of target sequences with the profile are determined in advance, permitting an objective decision to be made as to whether a protein is likely to possess a structural motif.

Received on July 17, 1987; accepted on January 4, 1988

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