Discovery of non-induced patterns from sequences

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

Volumn 6282 LNBI, Issue , 2010, Pages 149-160

  Wong, Andrew K C ^a   Zhuang, Dennis ^a   Li, Gary C L ^a   Lee, En Shiun Annie ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

Author keywords

Sequence Pattern Discovery; Statistically Induced Patterns; Suffix Tree

Indexed keywords

DATA SETS; GENOMICS; PERFORMANCE EVALUATION; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SEQUENCE DATA; SEQUENCE PATTERNS; SIGNIFICANT IMPACTS; SIGNIFICANT PATTERNS; STATISTICALLY INDUCED PATTERNS; SUB-PATTERNS; SUFFIX-TREES; SYNTHETIC DATA; TRANSCRIPTION FACTOR BINDING SITES; LARGE SEQUENCES;

BINDING ENERGY; BINDING SITES; BIOCHEMISTRY; MOLECULAR BIOLOGY; PATTERN RECOGNITION; QUALITY ASSURANCE; REDUNDANCY; TRANSCRIPTION FACTORS; YEAST; BIOINFORMATICS;

BIOINFORMATICS; PATTERN RECOGNITION;

EID: 78049472100     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-16001-1_13     Document Type: Conference Paper

References (16)

1. Rigoutsos, I., Floratos, A.: Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics 14(1), 55-67 (1998) (Pubitemid 28397726)
2. Parida, L., Rigoutsos, I., Floratos, A., Platt, D., Gao, Y.: Pattern Discovery on Character Sets and Real-valued Data: Linear Bound on Irredundant Motifs and an Efficient Polynomial Time Algorithm. In: Proceedings of the eleventh ACM-SIAM Symposium on Discrete Algorithms, pp. 297-308 (January 2000)
3. Sinha, S., Tompa, M.: Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Research 30(24), 5549-5560 (2002) (Pubitemid 36113932)
4. Apostolico, A., Bock, M., Lonardi, S., Xu, X.: Efficient Detection of Unusual Words. Journal of Computational Biology 7(1/2), 71-94 (2000)
5. Eskin, E., Pevzner, P.: Finding composite regulatory patterns in DNA sequences. Bioinformatics 18(suppl. 1), S354-S363 (2002)
6. Marsan, L., Sagot, M.: Extracting structured motifs using a suffix tree - Algorithms and application to promoter consensus identification. Journal of Computational Biology 7(3/4), 345-362 (2000)
7. Blanchette, M., Sinha, S.: Separating real motifs from their artifacts. Bioinformatics 17(suppl. 1), S30-S38 (2001)
8. Sze, S., Lu, S., Chen, J.: Integrating Sample-Driven and Pattern-Driven Approaches in Motif Finding. In: Algorithms in Bioinformatics: 4th International Workshop, pp. 438-449 (2004)
9. Bailey, T.L., Elkan, C.: Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 21, 51-80 (1995)
10. Pavesi, G., Zambelli, F., Pesole, G.: WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. BMC Bioinformatics 8, 46 (2007)
11. Haberman, S.: The Analysis of Residuals in Cross-Classified Tables. Biometrics 29, 205-220 (1973)
12. Wong, A., Wang, Y.: High-Order Pattern Discovery from Discrete-Valued Data. IEEE Trans on Knowledge Systems 9(6), 877-893 (1997)
13. Gusfield, D.: Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology (1997)
14. SCPD database, http://rulai.cshl.edu/SCPD/
15. Tompa, M., Li, N., Bailey, T., Church, G., Moor, B., Eskin, E., Favorov, A., Frith, M., Fu, Y., Kent, W., Makeev, V., Mironov, A., Noble, W., Pavesi, G., Pe-sole, G., Regnier, M., Simonis, N., Sinha, S., Thijs, G., Helden, J., Vandenbogaert, M., Weng, Z., Workman, C., Ye, C., Zhu, Z.: Assessing Computational Tools for the Discovery of Transcription Factor Binding Sites. Nature Biotechnology 23(1), 137-144 (2005) (Pubitemid 41724640)
16. Wong, A., Li, G.: Simultaneous Pattern Clustering and Data Grouping. IEEE Trans. Knowledge and Data Engineering 20(7), 911-923 (2008)