Similarity analysis of sequences belonging to some protein families indicates the existence of highly variable
positions. In this work, a method of interpretation of variability at these positions is presented. The proposed method
extends out of the Dot-Matrix method with the possibility of making new analysis of similarity and consideration of
physicochemical aspects of variability. These analyses have been made at two consideration levels, i.e. the amino-acid
level and codon level. To make this possible, semihomologization and desemihomologization mechanisms have been
introduced. As a result, the method of selection of sequences, which best represents the given protein family, has been
proposed. A higher frequency of six-codon amino-acids at the highly variable positions has been identified, which can
indicate that one-point mutation is the main mechanism of amino-acid codon evolution.
Keywords: Amino-acid level, codon level, cryptic mutations, multiple alignment, one-point mutation, protein similarity.
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