Motif discovery by monotone scores

Discrete Applied Mathematics

Volumn 155, Issue 6-7, 2007, Pages 695-706

  Apostolico, Alberto ^a,b   Pizzi, Cinzia ^a,c  

^a UNIVERSITY OF PADOVA   (Italy)

^b Georgia Institute of Technology   (United States)

^c UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Correction factor; Design and analysis of algorithms; Monotone score; Motif; Over represented word; Pattern discovery; Pattern matching

Indexed keywords

ALGORITHMS; COMPUTATIONAL COMPLEXITY; DIFFERENTIATION (CALCULUS); ERROR ANALYSIS; ERROR CORRECTION; MATHEMATICAL MODELS; PATTERN MATCHING; PROBABILITY;

CORRECTION FACTOR; MONOTONE SCORES; MOTIFS; OVER REPRESENTED WORDS; PATTERN DISCOVERY;

COMPUTATIONAL METHODS;

EID: 33846878040     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dam.2005.09.017     Document Type: Article

References (18)

1. Apostolico A. Pattern discovery and the algorithmics of surprise. In: Frasconi P., and Shamir R. (Eds). Artificial Intelligence and Heuristic Methods for Bioinformatics (2003), IOS Press 111-127
2. Apostolico A., Bock M.E., Lonardi S., and Xu X. Efficient detection of unusual words. J. Comput. Biol 7 1/2 (2000) 71-94
3. A. Apostolico, M.E. Bock, S. Lonardi, Monotony of surprise and large-scale quest for unusual words (extended abstract), in: G. Myers, S. Hannenhalli, S. Istrail, P. Pevzner, M. Waterman (Eds.), Proc. Research in Computational Molecular Biology (RECOMB), Washington, DC, April 2002, also in J. Comput. Biol., 10(3-4) (2003) 283-311.
4. A. Apostolico, Z. Galil (Eds.), Pattern Matching Algorithms, Oxford University Press, Oxford, 1997.
5. A. Apostolico, C. Pizzi, Monotone scoring of patterns with mismatches (extended abstract), in: Proc. Fourth Workshop on Algorithms in Bioinformatics (WABI 2004), Bergen, Norway, September 2004, Lecture Notes in Computer Science, vol. 3240, Springer, Berlin, 2004, pp. 87-98.
6. Bailey T.L., and Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Mach. Learn. 21 1/2 (1995) 51-80
7. Brāzma A., Jonassen I., Ukkonen E., and Vilo J. Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8 11 (1998) 1202-1215
8. Buhler J., and Tompa M. Finding motifs using random projections. J. Comput. Biol. 9 2 (2002) 225-242
9. R. Cole, L.A. Gottlieb, M. Lewenstein, Dictionary matching and indexing with errors and don't cares, in: Proc. of the thirty-sixth annual ACM Symposium on Theory of Computing (STOC), Chicago, IL, June 2004, pp. 91-100.
10. Gusfield D. Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology (1997), Cambridge University Press, Cambridge
11. van Helden J., André B., and Collado-Vides J. Extracting regulatory sites from the upstream region of the yeast genes by computational analysis of oligonucleotides. J. Mol. Biol. 281 (1998) 827-842
12. Hertz G.Z., and Stormo G.D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15 (1999) 563-577
13. Jonassen I. Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci. 13 (1997) 509-522
14. U. Keich, P.A. Pevzner, Finding motifs in the twilight zone, in: Annu. Internat. Conf. on Computational Molecular Biology, Washington, DC, April 2002, pp. 195-204.
15. Lawrence C.E., Altschul S.F., Boguski M.S., Liu J.S., Neuwald A.F., and Wootton J.C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262 (1993) 208-214
16. Leung M.Y., Marsh G.M., and Speed T.P. Over and underrepresentation of short DNA words in herpesvirus genomes. J. Comput. Biol. 3 (1996) 345-360
17. M. Lewenstein, Personal communication.
18. Pevzner P.A., and Sze S.-H. Combinatorial approaches to finding subtle signals in DNA sequences. Proc. Internat. Conf. on Intelligent Systems for Molecular Biology (2000), AAAI Press, Menlo Park,CA 269-278