DNA Sequence Assembly using Particle Swarm Optimization

DNA sequence assembly problem is a very complex problem of computational biology. DNA sequence assembly is a NP hard problem there is no single solution available for this kind of problems. DNA sequence assembly refers to aligning and merging fragments of a much longer DNA sequence in order to reconstruct the original sequence. In this paper a solution is proposed for DNA sequence assembly problem using Particle Swarm Optimization (PSO) with Shortest Position Value (SPV) rule. DNA sequence assembly problem is a discrete optimization problem, so there is need of discrete optimization algorithm to solve it. In this paper continuous version of PSO is used with SPV rule to solve the DNA sequence assembly problem. SPV rule transforms continuous version of PSO to discrete version. Proposed methodology is named as DSAPSO. To check the efficiency of proposed methodology the results of DSAPSO is compared with the results of genetic algorithm (GA). General Terms Nature Inspired Algorithms, optimization problem, Computational Biology.

[1]  Chilukuri K. Mohan,et al.  Parallel hierarchical adaptive genetic algorithm for fragment assembly , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[2]  C. Burks,et al.  DNA sequence assembly , 1994, IEEE Engineering in Medicine and Biology Magazine.

[3]  Jude W. Shavlik,et al.  Improving the Quality of Automatic DNA Sequence Assembly Using Fluorescent Trace-Data Classifications , 1996, ISMB.

[4]  Sami Khuri,et al.  A fast shotgun assembly heuristic , 2005, 2005 IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW'05).

[5]  Enrique Alba,et al.  Metaheuristics for the DNA Fragment Assembly Problem , 2005 .

[6]  Mark E. Johnson,et al.  DNA Sequence Assembly and Genetic Algorithms - New Results and Puzzling Insights , 1995, ISMB.

[7]  Owen White,et al.  TIGR Assembler: A New Tool for Assembling Large Shotgun Sequencing Projects , 1995 .

[8]  Goutam Chakraborty,et al.  Heuristically Tuned GA to Solve Genome Fragment Assembly Problem , 2006, 2006 IEEE International Conference on Evolutionary Computation.

[9]  X. Huang,et al.  CAP3: A DNA sequence assembly program. , 1999, Genome research.

[10]  Stephanie Forrest,et al.  Genetic Algorithms for DNA Sequence Assembly , 1993, ISMB.

[11]  Steven Skiena,et al.  Trie-Based Data Structures for Sequence Assembly , 1997, CPM.

[12]  Riccardo Poli,et al.  Particle swarm optimization , 1995, Swarm Intelligence.

[13]  Stephanie Forrest,et al.  Genetic algorithms, operators, and DNA fragment assembly , 1995, Machine Learning.

[14]  R. Eberhart,et al.  Comparing inertia weights and constriction factors in particle swarm optimization , 2000, Proceedings of the 2000 Congress on Evolutionary Computation. CEC00 (Cat. No.00TH8512).

[15]  Yong Wang,et al.  A Genetic Algorithm Approach to Solving DNA Fragment Assembly Problem , 2005 .

[16]  Nachol Chaiyaratana,et al.  DNA fragment assembly using an ant colony system algorithm , 2003, The 2003 Congress on Evolutionary Computation, 2003. CEC '03..

[17]  Yue Shi,et al.  A modified particle swarm optimizer , 1998, 1998 IEEE International Conference on Evolutionary Computation Proceedings. IEEE World Congress on Computational Intelligence (Cat. No.98TH8360).

[18]  Pavel A. Pevzner,et al.  Computational molecular biology : an algorithmic approach , 2000 .

[19]  Eugene W. Myers,et al.  Toward Simplifying and Accurately Formulating Fragment Assembly , 1995, J. Comput. Biol..

[20]  Ping Ma,et al.  An Improved Ant Colony Algorithm for DNA Sequence Alignment , 2008, 2008 International Symposium on Information Science and Engineering.