Finding consensus by sequence evolution: An application of Differential evolution

Author

Dongardive, Jyotshna ; Abraham, S.

Author_Institution

Dept. of Comput. Sci., Univ. of Mumbai, Mumbai, India

fYear

2012

fDate

Oct. 30 2012-Nov. 2 2012

Firstpage

248

Lastpage

253

Abstract

The paper proposes a novel idea of finding consensus of biological sequences using sequence evolution. It involves application of meta-heuristic optimization technique called Differential Evolution for the creation of a population of evolved sequences. This evolved population of sequences is used to find consensus using Position Frequency Matrix. DNA Sequences of highly risk HPV16 of Human pappilomavirus are used for the experimental purpose. A unique encoding procedure is used to encode the sequence of nucleotides to integers, making different Differential evolution operations possible. The experimental results validate the effectiveness of finding consensus from an evolved population sequences rather than finding the same from a known collection of sequences.

Keywords

DNA; biology computing; encoding; evolution (biological); microorganisms; molecular biophysics; molecular configurations; optimisation; DNA sequences; HPV16; biological sequences; consensus finding; differential evolution application; evolved sequences population; human pappilomavirus; metaheuristic optimization technique; nucleotide sequence; position frequency matrix; sequence evolution; unique encoding procedure; Communications technology; Decision support systems; Mercury (metals); US Department of Defense; Consensus; Conserved Region; DNA Sequence; Differential Evolution; Fitness Function; Human Papillomavirus; Multiple Sequence Alignment; Sequence Evolution;

fLanguage

English

Publisher

ieee

Conference_Titel

Information and Communication Technologies (WICT), 2012 World Congress on

Conference_Location

Trivandrum

Print_ISBN

978-1-4673-4806-5

Type

conf

DOI

10.1109/WICT.2012.6409083

Filename

6409083