The rapid generation of mutation data matrices from protein sequences
1Biomolecular Structure and Modelling Unit, Department of Biochemistry and Molecular Biology, University College Gower Street, London WCIE 6BT
2Laboratory of Mathematical Bioiogy, National Institute for Medical Research The Ridgeway. Mill Hill, London, NW7 IAA. UK
An efficient means for generating mutation data matrices from large numbers of protein sequences is presented here. By means of an approximate peptide-based sequence comparison algorithm, the set sequences are clustered at the 85% identity level. The closest relating pairs of sequences are aligned, and observed amino acid exchanges tallied in a matrix. The raw mutation frequency matrix is processed in a similar way to that described by Dayhoffet al. (1978), and so the resulting matrices may be easily used in current sequence analysis applications, in place of the standard mutation data matrices, which have not been updated for 13 years. The method is fast enough to process the entire SWISS-PROT databank in 20 h on a Sun SPARCstation 1, and is fast enough to generate a matrix from a specific family or class of proteins in minutes. Differences observed between our 250 PAM mutation data matrix and the matrix calculated by Dayhoff et al. are briefly discussed.
Received on October 21, 1991; accepted on December 6, 1991
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