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© IRL Press

SOMAP: a novel interactive approach to multiple protein sequences alignment

D.J. Parry-Smith and T.K. Attwood

Astbury Department of Biophysics and Department of Genetics, University of Leeds Leeds LS2 9JT, UK

A novel interactive method for generating multiple protein sequence alignments is described. The program has no internal limit to the number or length of sequences it can handle and is designed for use with DEC VAX processors running the VMS operating system. The approach used is essentially one of manual sequence manipulation, aided by built-in symbolic displays of identities and similarities, and strict and ‘fuzzy’ (ambiguous) pattern-matching facilities. Additional flexibility is provided by means of an interface to a publicly available automatic alignment system and to a comprehensive sequence analysis package.

Received on August 28, 1990; accepted on November 20, 1990

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