Voting algorithms for discovering long motifs

Series on Advances in Bioinformatics and Computational Biology

Volumn 1, Issue , 2005, Pages 261-271

  Chin, Francis Y L ^a   Leung, Henry C M ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS;

CO-REGULATED GENES; PROMOTER REGION; RUNNING TIME; SIMILAR PATTERN; SPACE REQUIREMENTS; VOTING ALGORITHM;

HAMMING DISTANCE;

EID: 84856991447     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1142/9781860947322_0026     Document Type: Conference Paper

References (19)

1. Timothy Bailey and Charles Elkan. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21:51-80, 1995
2. Alvis Brazma, Inge Jonassen, Ingvar Eidhammer, and David Gilbert. Approaches to the automatic discovery of patterns in biosequences. JCB, 5:279-305, 1998. (Pubitemid 28323817)
3. Jeremy Buhler and Martin Tompa. Finding motifs using random projections. RECOMB01, p69-76, 2001. (Pubitemid 32866142)
4. Norishige Chiba and Takao Nishizeki. Arboricity and Subgraph Listing Algorithm. SIAM Journal on Computing, 14:210-223, 1985
5. Y. Fraenkel, Y. Mandel, D. Friedberg, and H. Margalit. Identification of common motifs in unaligned dna sequences: application to Escherichia coli Lrp regulon. Bioinformatics, 11:379-387, 1995.
6. M. Gelfand, E. Koonin, and A. Mironov. Prediction of transcription regulatory sites in archaea by a comparative genomic approach. Nucl. Acids Res., 28:695-705, 2000. (Pubitemid 30068252)
7. J. van Helden, B. Andre, and J. Collado-Vides. Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology, 281(5):827-842, 1998. (Pubitemid 28408432)
8. G. Z. Hertz and G. D. Stormo. Identification of consensuspatterns in unaligned dna and protein sequences: a large-deviation statistical basis for penalizing gaps. The 3rd International Conference on Bioinformatics and Genome Research, p201-216, 1995
9. Charles Lawrence, Stephen Altschul, Mark Boguski, Jun Liu,Andrew Neuwald and John Wootton. Detecting subtule sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262:208-214, 1993
10. C. Lawrence and A. Reilly. An expectation maximization (em)algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins: Structure, Function and Genetics, 7:41-51, 1990 (Pubitemid 20102601)
11. Ming Li, Bin Ma, and Lusheng Wang. Finding similar regions in many strings. Journal of Computer and System Sciences, 65:73-96,2002
12. Shoudan Liang. cWINNOWER Algorithm for Finding Fuzzy DNA Motifs. Computer Society Bioinformatics Conference, p260-265, 2003
13. G. Pesole, N. Prunella, S. Liuni, M. Attimonelli, and C. Saccone. Wordup: an efficient algorithm for discovering statistically significant patterns in dna sequences. Nucl. Acids Res., 20(11):2871-2875,1992.
14. Pavel Pevzner and Sing-Hoi Sze. Combinatorial approaches to finding subtle signals in dna sequences. In Proc. of the Eighth International Conference on Intelligent Systems for Molecular Biology, p269-278, 2000.
15. Marie-France Sagot. Spelling approximate repeated or common motifs using a suffix tree. In C.L. Lucchesi and A.V. Moura editors, Latin'98: Theoretical informatics, volume 1380 of Lecture Notes in Computer Science, p111-127, 1998.
16. Roger Staden. Methods for discovering novel motifs in nucleic acid sequences. Computer Applications in Biosciences, 5(4):293-298, 1989 (Pubitemid 19274602)
17. Martin Tompa. An exact method for finding short motifs in sequences with application to the ribosome binding site problem. In Proc. of the 7th International Conference on Intelligent Systems for Molecular Biology, p262-271, 1999.
18. F. Wolfertsteeter, Kornelie Frech, Grit Herrmann, and Thomas. Wernet. Identification of functional elements in unaligned nucleic acid sequences by a novel tuple search algorithm. Computer Applications in Bio-sciences, 12(1):71-80, 1996. (Pubitemid 26095190)
19. Jian Zhu and Michael Zhang. SCPD: a promoter database of the yeast Saccha-romyces cerevisiae. Bioinformatics 15:563-577, 1999. http://cgsigma.cshl. org/jian/