Algorithm to find distant repeats in a single protein sequence.

Nirjhar Banerjee,Rangarajan Sarani,Chellamuthu Vasuki Ranjani,Narayanasamy Balakrishnan,Govindaraj Sowmiya,Daliah Michael,Kanagaraj Sekar

doi:10.6026/97320630003028

Abstract

Distant repeats in protein sequence play an important role in various aspects of protein analysis. A keen analysis of the distant repeats would enable to establish a firm relation of the repeats with respect to their function and three-dimensional structure during the evolutionary process. Further, it enlightens the diversity of duplication during the evolution. To this end, an algorithm has been developed to find all distant repeats in a protein sequence. The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats. Due to the biological importance of distant repeats, the proposed algorithm will be of importance to structural biologists, molecular biologists, biochemists and researchers involved in phylogenetic and evolutionary studies.

Highlights

The scores from Point Accepted Mutation (PAM) matrix has been deployed for the identification of amino acid substitutions while detecting the distant repeats
Distant repeats are evolved by duplication and recombination of genes, which gives rise to amino acid repeats within the protein sequence [1]
McLachlan and Stewart used Fourier transform analysis techniques [4, 11] which has been followed by the development of different techniques and algorithms by other groups to find the distant repeats amino acid residues

Summary

Introduction

Distant repeats are evolved by duplication and recombination of genes, which gives rise to amino acid repeats within the protein sequence [1]. Andrade and co-workers examined the important differences between certain protein families in order to study their evolution, structure, and function [2]. To understand more about the structural and functional relationship of the repeats in protein sequences, many types of repeats such as Ankyrin repeats, Armadillo repeats, HEAT repeats, TPR repeats, HAT repeats, Kelch repeats, Leucinerich repeats etc., have been studied in detail [3]. To get better understanding of these repeats, several algorithms have been derived to find amino acid repeats in protein sequences [4,5,6,7,8,9]. McLachlan and Stewart used Fourier transform analysis techniques (autocorrelation techniques) [4, 11] which has been followed by the development of different techniques and algorithms by other groups to find the distant repeats amino acid residues

Methods

Conclusion