A novel method for similarity/dissimilarity analysis of protein sequences

Sequence comparison is one of the major tasks in bioinformatics, which can be used to study structural and functional conservation, as well as evolutionary relations among the sequences. In this paper, we introduce the concept of distance frequency of amino acid pairs and propose a new numerical characterization of protein sequences, which converts any protein sequence into a distance frequency matrix. Using this distance frequency matrix, we can compare the similarity of protein sequences. In order to confirm the validity of our method, we test it with two experiments. The results show that our method is effective.