Building consensus of Human Papillomavirus using Genetic Algorithm

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.

Predicting 3D structure of proteins from genomic sequences: A genetic algorithm approach

“…Though there are many ways to predict the 3D structure of proteins, the authors have not come across any works using consensus sequences. The works done by Aditya et al [21] and Jyotshna et al [22] can be compared to a certain extent with the proposed work as they have used Genetic Algorithm and Differential Evolution respectively for finding consensus of genomic sequences. However, this work goes beyond their scope and tries to predict the 3D structure of proteins.…”

“…The resultant population, which is an evolved and optimized population, is used as a base to build the consensus. The consensus of the evolved sequences is found using Weight Matrix Algorithm [23] and IUBIUPAC code [24] as explained in [21] and [22].…”