Accelerated method for comparing amino acid sequences with allowance for possible gaps. Plotting optimum correspondence paths.
An accelerated method is suggested which enables an effective comparison to be made of amino acid (nucleotide) sequences of great length with due regard to a large number of possible gaps. The method consists in limiting the area of complete similarity charts, calculated in accordance with the algorithm suggested by Sankoff (1972), by a certain specially selected diagonal band. The application of the Monte-Carlo method permits a statistical evaluation to be made of the certainty of the similarity of the compared sequences and to choose on such a "comparison band", an optimum "correspondence path" which can readily be transformed into sequence alignment. Using this approach, prolactin and somatotropin families of sequences were found to be homologous at a high level of significance and their optimum alignment with two gaps has been suggested. In contrast, two regions of assumed partial gene duplication in beta-galactosidase sequence, suggested by Hood et al. (1978), were found not to be statistically significantly similar.