The week's pick
Random Articles
Reseach Article
An Improved Immune Genetic Algorithm for Weak Signal Motif Detecting Problems
| International Journal of Computer Applications |
| Foundation of Computer Science (FCS), NY, USA |
| Volume 43 - Number 15 |
| Year of Publication: 2012 |
| Authors: Xun Wang, Zhongyu Wang, Tao Song |
10.5120/6180-8609
|
Xun Wang, Zhongyu Wang, Tao Song . An Improved Immune Genetic Algorithm for Weak Signal Motif Detecting Problems. International Journal of Computer Applications. 43, 15 ( April 2012), 23-27. DOI=10.5120/6180-8609
Abstract
Motif detecting in DNA sequences is one of the most popular tasks in computational biology, which is important for people to understand functions of genes. Recently, the motif detecting problem was abstracted as a planted (l,d)-motif problem and many instances of the problem have been proposed as challenges for motif detecting algorithms. In this work, we propose an improved immune genetic algorithm, called MRPIGA, to solve a class of specific planted (l,d)-motif problems, weak signal motif problems, in which a modified random projection strategy is applied to generate a good initial population of candidate solutions. Experimental results on stimulated data show that MRPIGA performs better than Random Projection, GARPS and MDGA. We also test the MRPIGA on five groups of realistic biological data. It shows that the MRPIGA performs superior to detect motifs.
References
- Galas D. J. , Schmitz A. , 1978. A DNA footprinting: a simple method for the detection of protein-dna binding specifility, Nuleic Acids Res, 5, 9, (1978), 3157-3170.
- Garner M. M. , Revzin A. , 1981. A gel electrophoresis method for quantifying the binding of protein to specific DNA regions: application to components of the escherichia coli locates operon regulary system. Nucleic Acids Research, 9, 13, (1981), 3047-3060.
- Buhler J. , Tompa M. , 2001. Finding motifs using random projections. Journal of Computational Biology, 9, (2001), 225-242.
- Evans P. , Smith A. , 2003. Toward optimal motif enumeration. In Proceedings of Algorithms and Data Structures of Eighth International Workshop, WADS2003}, (2003), 47-58.
- Eskin E. , Pevzner P. , 2002. Finding composite regulatory patterns in DNA sequences. Bioinformatics S1, (2002), 354-363.
- Rajasekaran S. , Balla S, Huang C. H. , 2005. Exact algorithms for the planted motif problem. Journal of Computational Biology, 12, 8, (2005), 1117-1128.
- Davila J. , Balla S. , Rajasekaran S. , 2006. Space and time efficient algorithms for planted motif search. In Proceedings of the Second International Workshop on Bioinformatics Research and Applications (IWBRA 2006), (2006), 822-829.
- Marsan L. , Sagot M. F. , 2000. Extracting structured motifs using a suffix-tree. Algorithms and Application to Promoter Consensus Identification. In Proceedings of RECOMB2000, Tokyo, (2000), ACM Press.
- Bailey T. L. , Elkan C. , 1994. Fitting a mixture model by expectation maximization to discover motif in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, Menlo Park, CA, (1994), 28-36, AAAI Press.
- Liu X. , Brutlag D. L. , Liu J. S. , 2001. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes, Pacific Symposium on Biocomputing, 6, (2001), 127-138.
- Liu F. F. M. , Tsai J. J. P. , Chen R. M. , Chen S. N. , Shih S. H. , 2004. FMGA: finding motifs by genetic algorithm, In Proceedings of Fourth IEEE Symposium on Bio- informatics and Bioengineering, BIBE 2004, (2004), 459-466.
- Wei Z. , Jensen S. T. , 2006. GAME: detecting cis-regulatory elements using a genetic algorithm, Bioinform atisc, 22, 13, (2006), 1157-1184.
- Che D. , Zhao H. , Song Y. , 2005. MDGA: motif discovery using a genetic algorithm. In Proceedings of the 2005 Conference on Genetic and Evolutionary Computation (GECCO 2005), (2005), 447-452.
- Huo H. , Zhao Z. , Stojkovic V. , Liu L. , 2010. Optimizing genetic algorithm for motif discovery, Mathematical and Computer Modeling, 52, (2010), 2011-2020.
- Luo J. W. , Wang T. , 2010. Motif discovery using an immune genetic algorithm, Journal of Theoretical Biology,(2010), 264, 2, 319-325.
- Pevzner P. , Sze S. H. , 2000. Combinatorial approaches to binding subtle signals in DNA sequences. In Proceedings of Eighth International Conference on Intelligent Systems for Molecular Biology, (2000), 269-278.
- Rajasekaran S. , Balla, S, Huang C. H. , 2005. Exact algorithms for the planted motif problem, Journal of Computational Biology, 12, 8, (2005), 1117-1128.
Index Terms
Keywords