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Introducing variable gap penalties to sequence alignment in linear space

The problem of finding an optimal sequence alignment has been solved by Hirschberg (1975) in quadratic time and linear space. Myers and Miller (1988) presented an implementation of this algorithm for aligning biological sequences, incorporating affine gap penalties. The algorithm, has been essential in allowing progressive multiple sequence alignments to be performed on microcomputers with limited memory capacity. This paper presents a further development of the Myers and Miller algorithm. Here, we maximize similarity scores and, more significantly, introduce position-specific gap penalties. Thus, residue-dependent information such as structure preferences and existing gaps in a partial alignment can be applied to the solution of the alignment problem.