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Applied Computational Intelligence and Soft Computing
Volume 2012 (2012), Article ID 945401, 11 pages
An Efficient Genome Fragment Assembling Using GA with Neighborhood Aware Fitness Function
Faculty of Software and Information Science, Iwate Prefectural University, Takizawa-mura, Iwate 020-0193, Japan
Received 12 March 2012; Accepted 11 May 2012
Academic Editor: Qiangfu Zhao
Copyright © 2012 Satoko Kikuchi and Goutam Chakraborty. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- J. C. Neil and P. A. Pavel, An Introduction to Bioinformatics Algorithms, A Bradford Book, 2004.
- Y. Li and J. C. Patra, “Genome-wide inferring gene-phenotype relationship by walking on the heterogeneous network,” Bioinformatics, vol. 26, no. 9, Article ID btq108, pp. 1219–1224, 2010.
- Y. Li and J. C. Patra, “Integration of multiple data sources to prioritize candidate genes using discounted rating system,” BMC Bioinformatics, vol. 11, no. 1, article S20, 2010.
- E. S. Lander, L. M. Linton, B. Birren et al., “Initial sequencing and analysis of the human genome,” Nature, vol. 409, no. 6822, pp. 860–921, 2001.
- T. Sasaki, “The map-based sequence of the rice genome,” Nature, vol. 436, no. 7052, pp. 793–800, 2005.
- J. D. Watson and F. H. C. Crick, “Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid,” Nature, vol. 171, no. 4356, pp. 737–738, 1953.
- P. A. Benjamin, Genetics—A Conceptual Approach, W.H.Freeman and Company, 2005.
- P. P. Vaidyanathan, “Genomics and proteomics: a signal processor's tour,” IEEE Circuits and Systems Magazine, vol. 4, no. 4, pp. 6–29, 2004.
- W. C. Warren, L. W. Hillier, J. A. Marshall Graves et al., “Genome analysis of the platypus reveals unique signatures of evolution,” Nature, vol. 453, no. 7192, pp. 175–183, 2008.
- F. Sanger, A. R. Coulson, G. F. Hong, D. Hill, and G. Petersen,, “Nucleotide sequence of bacteriophage λ DNA,” Journal of Molecular Biology, vol. 162, no. 4, pp. 729–773, 1982.
- M. Pop, “Shotgun sequence assembly,” Advances in Computers, vol. 60, pp. 193–248, 2004.
- M. T. Tammi, The Principles of Shotgun Sequencing and Automates Fragment Assembly, Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden, 2003.
- S. Kim, “A survey of computational techniques for genome sequencing,” Project Report, Korea Institute of Science and Technology Information, 2002.
- G. G. Sutton, O. White, M. D. Adams, and A. R. Kerlavage, “TIGR assembler: a new tool for assembling large shotgun sequencing projects,” Genome Science and Technology, vol. 1, pp. 9–19, 1995.
- K. Mita, M. Kasahara, S. Sasaki et al., “The genome sequence of silkworm, Bombyx mori,” DNA Research, vol. 11, no. 1, pp. 27–35, 2004.
- E. W. Myers, G. G. Sutton, A. L. Delcher et al., “A whole-genome assembly of Drosophila,” Science, vol. 287, no. 5461, pp. 2196–2204, 2000.
- X. Huang and A. Madan, “CAP3: A DNA sequence assembly program,” Genome Research, vol. 9, no. 9, pp. 868–877, 1999.
- P. Green, “Phrap documentation : algorithms,” Phred/Phrap/Consed System Home Page, April 2006, http://www.phrap.org/.
- L. Li and S. Khuri, “A comparison of DNA fragment assembly algorithms,” in Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS '04), pp. 329–335, June 2004.
- R. J. Parsons, S. Forrest, and C. Burks, “Genetic algorithms, operators, and DNA fragment assembly,” Machine Learning, vol. 21, no. 1-2, pp. 11–33, 1995.
- K. Kim and C. K. Mohan, “Parallel hierarchical adaptive genetic algorithm for fragment assembly,” IEEE Congress on Evolutionary Computation, vol. 1, pp. 600–607, 2003.
- E. Alba, G. Luque, and S. Khuri, “Assembling DNA fragments with parallel algorithms,” in Proceedings of IEEE Congress on Evolutionary Computation (CEC '05), vol. 1, pp. 57–64, September 2005.
- S. C. Fang, Y. Wang, and J. Zhong, “A genetic algorithm approach to solving DNA fragment assembly problem,” Journal of Computational and Theoretical Nanoscience, vol. 2, no. 4, pp. 499–505, 2005.
- M. L. Engle and C. Burks, “Artificially generated data sets for testing DNA sequence assembly algorithms,” Genomics, vol. 16, no. 1, pp. 286–288, 1993.
- S. Kikuchi and G. Chakraborty, “Efficient assembling of genome fragments using genetic algorithm enhanced by heuristic search,” in Proceedings of IEEE Congress on Evolutionary Computation (CEC '07), vol. 1, pp. 305–312, September 2007.
- J. Craig Venter, M. D. Adams, E. W. Myers et al., “The sequence of the human genome,” Science, vol. 291, no. 5507, pp. 1304–1351, 2001.
- K. Mita, “Initial sequence of the chimpanzee genome and comparison with the human genome,” Nature, vol. 437, no. 7055, pp. 69–87, 2005.
- G. M. Weinstock, G. E. Robinson, R. A. Gibbs et al., “Insights into social insects from the genome of the honeybee Apis mellifera,” Nature, vol. 443, no. 7114, pp. 931–949, 2006.
- E. Sodergren, G. M. Weinstock, E. H. Davidson et al., “The genome of the sea urchin Strongylocentrotus purpuratus,” Science, vol. 314, no. 5801, pp. 941–952, 2006.
- J. Setubal and J. Meidanis, Introduction to Computational Molecular Biology, PWS Publishing Company, 1997.
- T. F. Smith and M. S. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, 1981.
- Z. Michalewicz, Algorithms + Data Structures = Evolution Programs, Springer, 1999.
- The National Center for Biotechnology Information, Home page at http://www.phrap.org/.