Login

Journal Image
Current Bioinformatics
ISSN (Print): 1574-8936
ISSN (Online): 2212-392X
Epub Full Text Article
DOI: 10.2174/1574893609666140516010304      Price:  $95









Identification of Protein Family Representatives

img
Author(s): Andrzej Kasperski and Renata Kasperska
Abstract:
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 represent 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
Affiliation:
Faculty of Biological Sciences, Department of Biotechnology, University of Zielona Gora, ul. Szafrana 1, 65-516 Zielona Gora, Poland.