Guiding motif discovery by iterative pattern refinement

Proceedings of the ACM Symposium on Applied Computing

Volumn 1, Issue , 2004, Pages 162-166

  Wang, Zhiping ^a   Dalkilic, Mehmet ^a   Kim, Sun ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

Bioinformatics; Framework; Motif; Pattern

Indexed keywords

ADENOSINETRIPHOSPHATE; ALGORITHMS; ITERATIVE METHODS; MATHEMATICAL MODELS; MATRIX ALGEBRA; PROBABILITY DISTRIBUTIONS; PROTEINS; SIGNAL TO NOISE RATIO; STATISTICAL METHODS; THRESHOLD ELEMENTS;

BIOINFORMATICS; FRAMEWORK; MOTIF; PATTERN;

PATTERN RECOGNITION;

EID: 2442608748     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/967900.967934     Document Type: Conference Paper

References (12)

1. Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Second International Conference on Intelligent Systems for Molecular Biology (ISMB), pp. 28-36, 1994
2. Timothy L. Bailey and Michael Gribskov, "Combining evidence using p-values: application to sequence homology searches", Bioinformatics, Vol. 14, pp. 48-54, 1998.
3. Sigrist C.J., Cerutti L., Hulo N., Gattiker A., Falquet L., Pagni M., Bairoch A., Bucher P, 'PROSITE: a documented database using patterns and profiles as motif descriptors", Brief Bioinform, 3: 265-274, 2002.
4. Falquet L., Pagni M., Bucher P., Hulo N., Sigrist C.J, Hermann K., Bairoch A, 'The PROSITE database, its status in 2002", Nucleic Acids Res., 30: 235-238, 2002.
5. Irfan Gunduz, Sihui Zhao, Mehmet Dalkilic and Sun Kim, "Motif Discovery from Large Number of Sequences: A Case Study with Disease Resistance Genes in Arabidopsis thaliana", The 2003 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'03), pp 29-34, 2003.
6. http://www.expasy.org/prosite/
7. J. Gorodkin, L. J. Heyer, S. Brunak and G. D. Storno, "Displaying the information contents of structural RNA alignments: the structure logos", Comput. Appl. Biosci., Vol. 13, no. 6 pp 583-586, 1997.
8. Thijs G., Lescot M., Marchai K., Rombuats S., De Moor, B. Rouze P, Moreau Y., "A higher order background model improves the detection of regulatory elements by Gibbs Sampling", Bioinformatic, 17(12) pp. 1113-1127, 2001.
9. I.Jonassen, J.F.Collins, D.G.Higgins, "Finding flexible patterns in unaligned protein sequences," Protein Science 4, pp1587-1595, 1995
10. I. Rigoutsos and A. Floratos, "Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm," Bioinformatics 14: pp55-67, 1998
11. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin.F. and Higgins.D.G. (1997) "The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools." Nucleic Acids Research, 24:4876-4882.
12. http://www.cbs.dtu.dk/~gorodkm/appl/plogo.html