Title

Algorithm to find distant repeats in a single protein sequence

Authors

Nirjhar Banerjee¹, Rangarajan Sarani¹, Chellamuthu Vasuki Ranjani¹, Govindaraj Sowmiya¹, Daliah Michael¹, Narayanasamy Balakrishnan², Kanagaraj Sekar^{1, 2, *}

Affiliation

¹Bioinformatics Centre, Centre of Excellence in Structural Biology and Bio-computing; ²Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India

Email

sekar@physics.iisc.ernet.in; * Corresponding author

Phone

91-80-22933059

Fax

91-80-23600683

Article Type

Prediction Model

Date

received July 07, 2008; accepted July 24, 2008; published September 19, 2008

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.

Keywords

distant repeats; genome sequences; point accepted mutation; structure-function relationship; phylogeny

Citation

Banerjee et al., Bioinformation 3(1): 28-32 (2008)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.