Building consensus of Human Papillomavirus using Genetic Algorithm

Author

Bir, Aditya ; Dongardive, Jyotsna ; Jamkhedkar, Suruchi ; Abraham, Siby

Author_Institution

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

fYear

2009

fDate

9-11 Dec. 2009

Firstpage

818

Lastpage

823

Abstract

The paper introduces a novel three tier architecture to find consensus of Human Papillomavirus (HPV). The proposed procedure is based on simulation and uses all complete genomic DNA sequences of registered HPV strains available in NCBI GenBank. It uses the multiple sequence alignment tool Clustal X to align these sequences. Genetic Algorithm is used to evolve an optimized population of complete genomic DNA sequences. The GA, which uses domain specific genetic operators like migration, rank selection, mutation and crossover, adopts a novel approach in defining the fitness function. A modified approach of the Weight Matrix Algorithm is applied on the optimized and evolved population to find a consensus of HPV. The effectiveness of the procedure is validated with experimental results.

Keywords

DNA; biology computing; genetic algorithms; genetics; genomics; microorganisms; molecular biophysics; Clustal X; HPV strains; NCBI GenBank; consensus building; crossover; genetic algorithm; genetic operators; genomic DNA sequences; human Papillomavirus; migration; multiple sequence alignment tool; mutation; rank selection; weight matrix algorithm; Bioinformatics; Capacitive sensors; Cervical cancer; Computer science; DNA; Genetic algorithms; Genomics; Humans; Sequences; Vaccines;

fLanguage

English

Publisher

ieee

Conference_Titel

Nature & Biologically Inspired Computing, 2009. NaBIC 2009. World Congress on

Conference_Location

Coimbatore

Print_ISBN

978-1-4244-5053-4

Type

conf

DOI

10.1109/NABIC.2009.5393579

Filename

5393579