An algorithm for finding signals of unknown length in DNA sequences

Bioinformatics

Volumn 17, Issue SUPPL. 1, 2001, Pages

  Pavesi, Giulio ^a   Mauri, Giancarlo ^a   Pesole, Graziano ^b  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; EVALUATION; GENETIC PROCEDURES; GENETICS; NUCLEOTIDE SEQUENCE; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA; DNA MUTATIONAL ANALYSIS; GENETIC TECHNIQUES; PATTERN RECOGNITION, AUTOMATED; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 0035224579     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/17.suppl_1.S207     Document Type: Article

References (21)

1. Apostolico, A., Bock, M., Lonardi, S. & Xu, X. (2000). Efficient detection of unusual words. Journal of Computational Biology, 7, 71-94.
2. Bailey, T. & Elkan, C. (1995). Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 51-80.
3. Brazma, A., Jonassen, I., Vilo, J. & Ukkonen, E. (1998). Predicting gene regulatory elements in silico on a genomic scale. Genome Research, 8, 1202-1215.
4. Buhler, J. & Tompa, M. (2001). Finding motifs using random projections. In Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001). To appear.
5. Califano, A. (2000). Splash: structural pattern localization analysis by sequential histograms. Bioinfonnatics, 16, 341-357.
6. Gelfand, M., Koonin, E. & A.Mironov (2000). Prediction of transcription regulatory sites in arachea by a comparative genomic approach. Nucleic Acids Research, 28, 695-705.
7. Gusfield, D. (1997). Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge University Press, New York.
8. Hertz, G. & Stormo, G. (1999). Identifying dna and protein patterns with statistically significant alignment of multiple sequences. Bioinfonnatics, 15, 563-577.
9. Hui, L. (1992). Color set size with applications to string matching. In Proc. 3rd Symp. on Combinatorial Pattern Matching, Springer Verlag LNCS 644. pp. 227-240.
10. Lawrence, C., Altschul, S., Boguski, M., Liu, J., Neuwald, A. & Wooton, J. (1993). Detecting subtle sequence signals: a gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
11. Li, M., Ma, B. & Wang, L. (1999). Finding similar regions in many strings. In Proceedings of the 31st Annual ACM Symposium on Theory of Computing, pp. 473-482.
12. Marsan, L. & Sagot, M. (2000). Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification. Journal of Computational Biology, 7, 345-360.
13. McCreight, E. (1976). A space-economical suffix tree construction algorithm. Journal of the ACM, 23, 262-272.
14. Pesole, G., Prunella, N., Liuni, S., Attimonelli, M. & Saccone, C. (1992). Wordup: an efficient algorithm for discovering statistically significant patterns in dna sequences. Nucleic Acids Research, 20, 2871-2875.
15. Pevzner, P. & Sze, S.-H. (2000). Combinatorial approaches to finding subtle signals in dna sequences. In Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology.
16. Sagot, M. (1998). Spelling approximate repeated or common motifs using a suffix tree. Lecture Notes in Computer Science, 1380, 111-127.
17. Staden, R. (1989). Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in Biosciences, 5, 293-298.
18. Tompa, M. (1999). An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. In Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology.
19. Ukkonen, E. (1995). On-line construction of suffix trees. Algorithmica, 14, 249-260.
20. Weiner, P. (1973). Linear pattern matching algorithms. In Proc. of the 14th IEEE Symp. on Switching and Automata Theory, pp. 1-11.
21. Wolferstetter, F., Frech, K., Herrmann, G. & Werner, T. (1996). Identification of functional elements in unaligned nucleic acids sequences by a novel tuple search algorithm. Computer Applications in Biosciences, 12, 71-80.