A survey on merging DNA fragments using soft computing algorithm

DNA material is present in all living things and it contains all relative information. DNA material is very long in nature and contains more than 10,000 base pairs. These base pairs contains mainly four element i.e. adenine (A), guanine (G), cytosine(C), thymine (T). To study DNA directly is very difficult task. DNA fragmentation is the separation or breaking of DNA strands into pieces. DNA fragmentation helps in analyzing or processing on DNA fragments. After DNA fragmentation, it requires reconstruction to form original DNA to identify the living thing. Research has shown that the problems like Computational errors, Unknown origin of DNA, Repetition of similar sequence occur while reconstructing the fragments into the original one. To solve or minimize these problems many researchers have proposed different methods. In this paper, several methods are discussed as well as reviewed. Also a new method is proposed. The Proposed algorithm is based on Particle Swarm Optimization (PSO).

[1]  Hesham Ahmed Hefny,et al.  Chaotic particle swarm optimization , 2010, 2010 The 7th International Conference on Informatics and Systems (INFOS).

[2]  Enrique Alba,et al.  A Hybrid Genetic Algorithm for the DNA Fragment Assembly Problem , 2008, Recent Advances in Evolutionary Computation for Combinatorial Optimization.

[3]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[4]  Jinglu Hu,et al.  Accurate Reconstruction for DNA Sequencing by Hybridization Based on a Constructive Heuristic , 2011, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[5]  Zenghui Wang,et al.  Chaotic particle swarm optimization , 2009, GEC '09.

[6]  Kumar Sanjay,et al.  DNA Sequence Assembly using Particle Swarm Optimization , 2011 .

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

[8]  Enrique Alba,et al.  SAX: a new and efficient assembler for solving DNA Fragment Assembly Problem , 2012 .

[9]  David Tse,et al.  Information Theory of DNA Shotgun Sequencing , 2012, IEEE Transactions on Information Theory.

[10]  Goutam Chakraborty,et al.  An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function , 2012, Appl. Comput. Intell. Soft Comput..

[11]  Guillermo Fernández-Anaya,et al.  DNA fragment assembly using optimization , 2013, 2013 IEEE Congress on Evolutionary Computation.

[12]  Enrique Alba,et al.  Metaheuristic assemblers of DNA strands: Noiseless and noisy cases , 2010, IEEE Congress on Evolutionary Computation.

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