Pairwise sequence alignment using a PROSITE pattern-derived similarity score.

J P Comet; J Henry

doi:10.1016/s0097-8485(02)00005-0

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Pairwise sequence alignment using a PROSITE pattern-derived similarity score.

J P Comet·J Henry

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Abstract

Existing methods for alignments are based on edition costs computed additionally position by position, according to a fixed substitution matrix: a substitution always has the same weight regardless of the position. Nevertheless the biologist favours a similarity according to his knowledge of the structure or the function of the sequences considered. In the particular case of proteins, we present a method consisting in integrating other information, such as patterns of the PROSITE databank, in the classical dynamic programming algorithm. The method consists in making an alignment by dynamic programming taking a decision not only letter by letter as in the Smith & Waterman algorithm but also by giving a reward when aligning patterns.

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Algorithms Amino Acid Motifs Amino Acid Sequence Databases, Genetic Molecular Sequence Data Pattern Recognition, Automated Proteins Sequence Alignment Software Software Design Journal Article

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BibTeX RIS

J P Comet, J Henry. 2002. Pairwise sequence alignment using a PROSITE pattern-derived similarity score.. https://doi.org/10.1016/s0097-8485(02)00005-0

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