Monotone scoring of patterns with mismatches (extended abstract)

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3240, Issue , 2004, Pages 87-98

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

^a PURDUE UNIVERSITY   (United States)

^b UNIVERSITY OF PADOVA   (Italy)

^c Purdue University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS;

CONSTANT FREQUENCY; ERROR THRESHOLD; K-MISMATCHES; MONOTONICITY CONDITIONS; PROBABILITY OF OCCURRENCE; SUB-STRINGS; SUBSTRING;

PROBABILITY;

EID: 35048832304     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30219-3_8     Document Type: Article

References (12)

1. APOSTOLICO, A. Pattern discovery and the algorithmics of surprise. In Artificial Intelligence and Heuristic Methods for Bioinformatics (2003), P. Frasconi and R. Shamir, Eds., IOS Press, pp. 111-127.
2. APOSTOLICO, A., AND GALIL, Z., Eds. Pattern matching algorithms. Oxford University Press, 1997.
3. APOSTOLICO, A., BOCK, M. E., AND LONARDI, S. Monotony of surprise and large-scale quest for unusual words (extended abstract). In Proc. of Research in Computational Molecular Biology RECOMB (Washington, DC, April 2002),
4. G. Myers, S. Hannenhalli, S. Istrail, P. Pevzner, and M. Waterman, Eds. Also, J. Comp. Bio., 10:3-4, (July 2003), 283-311.
5. APOSTOLICO, A., AND PARIDA, L. Incremental Paradigms of Motif Discovery. J. Comput. Bio. 7, 11:1, (Jan. 2004), 15-25.
6. BAILEY, T. L., AND ELKAN, C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21, 1/2 (1995), 51-80.
7. BRÄZMA, A., JONASSEN, I., UKKONEN, E., AND VILO, J. Predicting gene regulatory elements in silico on a genomic scale. Genome Research 8, 11 (1998), 1202-1215.
8. BUHLER, J., AND TOMPA, M. Finding motifs using random projections. J. Comput. Bio. 9, 2 (2002), 225-242.
9. HERTZ, G. Z., AND STORMO, G. D. Identifying DNA and protein patterns with statistically sign ificant alignments of multiple sequences. Bioinformatics 15 (1999), 563-577.
10. JONASSEN, I. Efficient discovery of conserved patterns using a pattern graph. Comput. Appl. Biosci. 13 (1997), 509-522.
11. KEICH, AND PEVZNER. Finding motifs in the twilight zone. In Annual International Conference on Computational Molecular Biology (Washington, DC, Apr. 2002), pp. 195-204.
12. 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 (Oct. 1993), 208-214.