VARUN: Discovering extensible motifs under saturation constraints

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 7, Issue 4, 2010, Pages 752-762

  Apostolico, Alberto ^a,b   Comin, Matteo ^b   Parida, Laxmi ^c  

^a Georgia Institute of Technology   (United States)

^b UNIVERSITY OF PADOVA   (Italy)

^c IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

computational genomics; Computational genomics; data mining; motif; pattern discovery; protein family.; protein sequence

Indexed keywords

GENOMICS; MOTIF; PATTERN DISCOVERY; PROTEIN FAMILY.; PROTEIN SEQUENCE;

DATA MINING; SYNTACTICS;

PROTEINS;

PROTEIN;

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; DATA MINING; METHODOLOGY; PROTEIN MOTIF; SEQUENCE ANALYSIS;

AMINO ACID MOTIFS; DATA MINING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE;

EID: 78149283787     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.123     Document Type: Article

References (20)

1. R. Agrawal and R. Srikant, "Fast Algorithms for Mining Association Rules," Proc. 20th Int'l Conf. Very Large Data Bases (VLDB), pp. 487-499, 1994.
2. A. Apostolico, M.E. Bock, and S. Lonardi, "Monotony of Surprise and Large Scale Quest for Unusual Words," J. Computational Biology, vol. 10, nos. 3/4, pp. 283-311, 2003.
3. A. Apostolico, M. Comin, and L. Parida, "Conservative Extraction of Over-Represented Extensible Motifs," Proc. Int'l Conf. Intelligent Systems for Molecular Biology (ISMB '05), Bioinformatics, vol. 21, no. 1, pp. 9-18, 2005.
4. A. Apostolico and L. Parida, "Incremental Paradigms for Motif Discovery," J. Computational Biology, vol. 11, no. 1, pp. 15-25, 2004.
5. A. Apostolico and C. Pizzi, "Monotone Scoring of Patterns with Mismatches," Proc. Workshop Algorithms in Bioinformatics (WABI), vol. 3240, pp. 87-98, Sept. 2004.
6. T. Bailey, N. Williams, C. Misleh, and W. Li, "MEME: Discovering and Analyzing DNA and Protein Sequence Motifs," Nucleic Acids Research, vol. 34, pp. W369-W373, 2006.
7. A. Blumer, J. Blumer, A. Ehrenfeucht, D. Haussler, M.T. Chen, and J. Seiferas, "The Smallest Automaton Recognizing the Subwords of a Text," Theoretical Computer Science, vol. 40, pp. 31-55, 1985.
8. D.R. Breiter, T.E. Meyer, I. Rayment, and H.M. Holden, J. Biological Chemistry, vol. 266, pp. 18660-18667, 1991.
9. J. Buhler and M. Tompa, "Finding Motifs Using Random Projections," J. Computational Biology, vol. 9, no. 2, pp. 225-242, 2002.
10. A. Chattaraj and L. Parida, "An Inexact Suffix Tree Based Algorithm for Extensible Pattern Discovery," Theoretical Computer Science, vol. 335, no. 1, pp. 3-14, 2005.
11. G.Z. Hertz and G.D. Stormo, "Identifying DNA and Protein Patterns with Statistically Significant Alignments of Multiple Sequences," Bioinformatics, vol. 15, pp. 563-577, 1999.
12. U. Keich and P.A. Pevzner, "Finding Motifs in the Twilight Zone" Proc. Ann. Int'l Conf. Computational Molecular Biology, pp. 195-204, Apr. 2002.
13. C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald, and J.C. Wootton, "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment," Science, vol. 262, pp. 208-214, Oct. 1993.
14. M.Y. Leung, G.M. Marsh, and T.P. Speed, "Over and Under-representation of Short DNA Words in Herpesvirus Genomes," J. Computational Biology, vol. 3, pp. 345-360, 1996.
15. L. Parida, Pattern Discovery in Bioinformatics: Theory and Algorithms. Chapman Hall/CRC, 2007.
16. P.A. Pevzner and S.-H. Sze, "Combinatorial Approaches to Finding Subtle Signals in DNA Sequences," Proc. Eighth Int'l Conf. Intelligent Systems for Molecular Biology, pp. 269-278, 2000.
17. I. Rigoutsos and A. Floratos, "Motif Discovery in Biological Sequences without Alignment or Enumeration," Proc. Ann. Conf. Computational Molecular Biology (RECOMB '98), pp. 221-227, 1998.
18. J.T.L. Wang, B.A. Shapiro, and D. Shasha, Pattern Discovery in Biomolecular Data. Oxford Univ. Press, 1999.
19. M.S. Waterman, An Introduction to Computational Biology: Maps, Sequences and Genomes. Chapman Hall, 1995.
20. J. Zhu and M. Zhang, "SCPD: A Promoter Database of the Yeast Saccha-Romyces Cerevisiae," Bioinformatics, vol. 15, pp. 607-611, 1999.