Finding optimal degenerate patterns in DNA sequences

Bioinformatics

Volumn 19, Issue SUPPL. 2, 2003, Pages

  Shinozaki, Daisuke ^a   Akutsu, Tatsuya ^b   Maruyama, Osamu ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BINDING SITE; CONFERENCE PAPER; DNA SEQUENCE; MATHEMATICAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; REGULON; SEQUENCE ALIGNMENT; YEAST;

EID: 14744270169     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg1079     Document Type: Conference Paper

References (23)

1. Bailey, T.L. and Elkan, C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 51-80.
2. Bannai, H., Inenaga, S., Shinohara, A., Takeda, M. and Miyano, S (2002) A string pattern regression algorithm and its application to pattern discovery in long introns. Genome Informatics 2002 (GIW2002), 3-11.
3. Blanchette, M. and Sinha, S. (2001) Separating real motifs from their artifacts. Bioinformatics, 17, S30-S38.
4. Buhler, J. and Tompa, M. (2002) Finding motifs using random projections. J. Comput. Biol., 9, 225-242.
5. Fellows, M.R., Gramm, J. and Niedermeier, R. (2002) On the parameterized intractability of closest substring and related problems. Proceedings of the 19th International Symposium on Theoretical Aspects of Computer Science (STACS 2002), Lecture Notes in Computer Science 2285, Springer-Verlag, pp. 262-273.
6. Gramm, J., Niedermeier, R. and Rossmanith, P. (2001) Exact solutions for Closest String and related problems. Proceedings of the 12th Annual International Symposium on Algorithms and Computation (ISAAC 2001), Lecture Notes in Computer Science, 2223, Springer, pp. 441-452.
7. Hertz, G.Z. and Stormo, G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
8. Lanctot, K., Li, M., Ma, B., Wang, S. and Zhang, L. (1999) Distinguishing string selection problems. Proceedings of the 10th Annual ACM-SIAM Symposium on Discrete algorithms (SODA 1999). pp. 633-642.
9. Lawrence, C., Altschul, S., Boguski, M., Liu, J., Neuwald, F. and Wootton, J. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
10. Lawrence, C. and Reilly, A. (1990) An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51.
11. Liu, X., Brutlag, D. and Liu, J. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of coexpressed genes. Pacific Symposium on Biocomputing. pp. 127-138.
12. Marsan, E. and Sagot, M.-F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol., 7, 345-362.
13. Maruyama, O., Bannai, H., Tamada, Y., Kuhara, S. and Miyano, S. (2002) Fast algorithm for extracting multiple unordered short motifs using bit operations. Information Sci., 146, 115-126.
14. Pavlidis, P., Furey, T., Liberto, M., Haussler, D. and Grundy, W. (2001) Promoter region-based classification of genes. Pac. Symp. Biocomput., 151-163.
15. Pevzner, P.A. and Sze, S.-H. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). pp. 269-278.
16. Roth, F., Hughes, J., Estep, P. and Church, G. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
17. Shinohara, A., Takeda, M., Arikawa, S., Hirano, M., Hoshino, H. and Inenaga, S. (2002) Finding best patterns practically. Progress in Discovery Science, Lecture Notes in Computer Science, 2281, Springer, pp. 307-317.
18. Sinha, S. (2002) Discriminative motifs. Proceedings of the 6th Annual International Conference on Computational Biology (RECOMB 2002). pp. 291-298.
19. Sinha, S. and Tompa, M. (2000) A statistical method for finding transcription factor binding sites. Proceedings of the 8th International Conference on Intelligent Systems for Molecular Biology (ISMB 2000). pp. 344-354.
20. Sinha, S. and Tompa, M. (2003) Performance comparison of algorithms for finding transcription factor binding sites. Proceedings of the 3rd IEEE Symposium on Bioinformatics and Bioengineering (BIBE 2003). pp. 214-220.
21. Tateishi, E., Maruyama, O. and Miyano, S. (1996) Extracting best consensus motifs from positive and negative examples. Proceedings of the 13th Annual Symposium on Theoretical Aspects of Computer Science (STACS 1996), Lecture Notes in Computer Science, 1046, Springer, pp. 219-230.
22. van Helden, J., André, B. and Collado-Vides, J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
23. Zhu, J. and Zhang, M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.