Current Bioinformatics

Alessandro Giuliani
Istituto Superiore di Sanitá (Italian NIH) Environment and Health Dept


Identification of Protein Family Representatives

Author(s): Andrzej Kasperski and Renata Kasperska

Affiliation: Faculty of Biological Sciences, Department of Biotechnology, University of Zielona Gora, ul. Szafrana 1, 65-516 Zielona Gora, Poland.


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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Article Details

Page: [414 - 425]
Pages: 12
DOI: 10.2174/1574893609666140516010304