Top-down motif discovery in biological sequence datasets by genetic algorithm

Proceedings - 2006 International Conference on Hybrid Information Technology, ICHIT 2006

Volumn 2, Issue , 2006, Pages 103-107

  Baloglu, Ulas Baran ^a   Kaya, Mehmet ^a  

^a FIRAT UNIVERSITY   (Turkey)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL COMPLEXITY; DATA STRUCTURES; GENETIC ALGORITHMS; STORAGE ALLOCATION (COMPUTER);

BIOSEQUENCES; COMPUTATIONAL BIOLOGY; DISCOVERY ALGORITHMS; SEQUENCE ALIGNMENT;

DATA MINING;

EID: 34247191985     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICHIT.2006.253597     Document Type: Conference Paper

References (11)

1. Keich, U. and Pevzner, P.A. "Finding motifs in the twilight zone", Bioinformatics, Vol.18, pp. 1374-1381, 2002.
2. Bailey, T.L. and Elkan, C. "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, AAAI Press, Menlo Park, California, pp. 28-36, 1994.
3. Thompson, W., Rouchka E.C. and Lawrence C.E. "Gibbs Recursive Sampler: Finding transcription factor binding sites", J. Nucleic Acids Research, Vol.31, pp. 3580-3585, 2003.
4. Hertz, G.Z., Hartzell, G.W. and Stormo, G.D. "Identification of consensus patterns in unaligned DNA sequences known to be functionally related", Bioinformatics, Vol.6, pp. 81-92, 1990.
5. Stine, M., Dasgupta, D. and Mukatira, S. "Motif Discovery in Upstream Sequences of Coordinately Expressed Genes", The 2003 Congress on Evolutionary Computation, pp. 1596-1603, 2003.
6. Liu, F.F.M et al. "FMGA: Finding Motifs by Genetic Algorithm", Proceedings of the Fourth IEEE Symposium on Bioinformatics and Bioengineering, pp.459-466, 2004.
7. Pan, J. et al. "Efficient Algorithms for Mining Maximal Frequent Concatenate Sequences in Biological Datasets", Proceedings of the Fifth International Conference on Computer and Information Technology, pp. 98-104, 2005.
8. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. "Basic local alignment search tool." J. Mol. Biol. 215:403-410, 1990.
9. Ester, M. and Zhang, X. "A Top-Down Method for Mining Most Specific Frequent Patterns in Biological Sequence Data", Proc. SIAM Int. Conf. on Data Mining (SDM'2004) 2004.
10. M. Scherf, A. Klingenhoff, T. Werner, "Highly Specific Localization of Promoter Regions in Large Genomic Sequences by PromoterInspector: A Novel Context Analysis Approach," J. Mol. Biol. 297 (3), pp. 599-606, 2000.
11. Horton, P., "Tsukuba BB: A Branch and Bound Algorithm for Local Multiple Alignment of DNA and Protein Sequences", Journal of Computational Biology, 8(3):pp.283-303, 2001.