{"title":"Multiple Sequence Alignment Using Optimization Algorithms","authors":"M. F. Omar, R. A. Salam, R. Abdullah, N. A. Rashid","volume":5,"journal":"International Journal of Computer and Information Engineering","pagesStart":1512,"pagesEnd":1521,"ISSN":"1307-6892","URL":"https:\/\/publications.waset.org\/pdf\/14036","abstract":"
Proteins or genes that have similar sequences are likely to perform the same function. One of the most widely used techniques for sequence comparison is sequence alignment. Sequence alignment allows mismatches and insertion\/deletion, which represents biological mutations. Sequence alignment is usually performed only on two sequences. Multiple sequence alignment, is a natural extension of two-sequence alignment. In multiple sequence alignment, the emphasis is to find optimal alignment for a group of sequences. Several applicable techniques were observed in this research, from traditional method such as dynamic programming to the extend of widely used stochastic optimization method such as Genetic Algorithms (GAs) and Simulated Annealing. A framework with combination of Genetic Algorithm and Simulated Annealing is presented to solve Multiple Sequence Alignment problem. The Genetic Algorithm phase will try to find new region of solution while Simulated Annealing can be considered as an alignment improver for any near optimal solution produced by GAs.<\/p>\r\n","references":"[1] N. M. Luscombe, D. Greebaum, M. Gerstein, (2001). What is\r\nbioinformatics? A proposed definition and overview of the field.\r\nDepartment of Molecular Biophysics and Biochemistry, Yale University,\r\nUSA.\r\n[2] R. Musick, T. Slezak, T. Crithlow, (2001). An Overview of\r\nBioinformatics Research at Lawrence Livermore National Laboratory.\r\nJoint Genome Institute \/ Computing Application Organization .Lawrence\r\nLivermore National Laboratory.\r\n[3] Online Lectures on Bioinformatics (September 2003) (Online),\r\nAvailable: http:\/\/lectures.molgen.mpg.de\/Biol\/index.html.\r\n[4] P. C. Turner, A. G. McLennan, A. D Bates, M. R. H. White, (1997).\r\nNucleic Acid Structure. Instant Notes in Molecular Biology C1:31-35.\r\nBios Scientific Publishers Limited, Liverpool.\r\n[5] M. 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