ACCELERATED METHOD FOR COMPARING AMINO ACID SEQUENCES WITH ALLOWANCE FOR POSSIBLE GAPS: Plotting Optimum Correspondence Paths

Abstract

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, 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 2 gaps was suggested. In contrast, 2 regions of assumed partial gene duplication in .beta.-galactosidase sequence, suggested by Hood et al, were not statistically significantly similar.