DSAPSO: DNA sequence assembly using continuous Particle Swarm Optimization with Smallest Position Value rule

Author

Verma, Ravi Shankar ; Kumar, Sanjay

Author_Institution

Dept. of Electr. Eng., Nat. Inst. of Technol., Raipur, India

fYear

2012

fDate

15-17 March 2012

Firstpage

410

Lastpage

415

Abstract

DNA sequence assembly is one of the most popular problems in molecular biology. DNA sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. There are many solutions provided by researchers. In this paper we have adopted the features of the Particle Swarm Optimization (PSO) algorithm with Smallest Position Value (SPV) rule and designed a sequential algorithm to solve DNA sequence assembly and named it DSAPSO. DNA sequence assembly problem is a discrete optimization problem, so there is need of discrete optimization algorithm to solve it. We use continuous version of PSO with SPV rule to solve the DNA sequence assembly problem. SPV rule transforms continuous version of PSO to discrete version. To check the efficiency of proposed methodology the results of DSAPSO is compared with the results of genetic algorithm (GA).

Keywords

bioinformatics; genetic algorithms; molecular biophysics; particle swarm optimisation; DNA sequence assembly problem; DSAPSO; GA; SPV; continuous particle swarm optimization; discrete optimization problem; fragment alignment; fragment merging; genetic algorithm; molecular biology; sequential algorithm; smallest position value rule; Algorithm design and analysis; Assembly; DNA; Genetic algorithms; Optimization; Particle swarm optimization; Vectors; Bioinformatics; DNA sequence assembly; PSO; Particle Swarm Optimization; SPV; Swarm Intelligence;

fLanguage

English

Publisher

ieee

Conference_Titel

Recent Advances in Information Technology (RAIT), 2012 1st International Conference on

Conference_Location

Dhanbad

Print_ISBN

978-1-4577-0694-3

Type

conf

DOI

10.1109/RAIT.2012.6194455

Filename

6194455