Abstract
An improved method for testing similarities or repeats in protein sequences is described. It includes three features: a measure of similarity for amino acids, based on observed substitutions in homologous proteins; a search procedure which compares all pairs of segments of two proteins; new statistical tests which estimate the probabilities that observed correlations could have occurred by chance. Calculations show that gene duplication has probably not occurred in plant ferredoxins; phage Qβ and f2 coat proteins may be homologous; and repeats in cytochrome c are not statistically significant. The method predicted an alignment of cytochrome c and c 551 sequences which later appeared consistent with Dickerson's atomic model of horse cytochrome c.
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