Title :
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
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;
Conference_Titel :
Recent Advances in Information Technology (RAIT), 2012 1st International Conference on
Conference_Location :
Dhanbad
Print_ISBN :
978-1-4577-0694-3
DOI :
10.1109/RAIT.2012.6194455
