VOMBAT: Prediction of transcription factor binding sites using variable order Bayesian trees

Nucleic Acids Research

Volumn 34, Issue WEB. SERV. ISS., 2006, Pages

  Grau, Jan ^c   Ben Gal, Irad ^a   Posch, Stefan ^c   Grosse, Ivo ^b  

^a TEL AVIV UNIVERSITY   (Israel)

^b LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^c MARTIN LUTHER UNIVERSITY HALLE WITTENBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; BAYES THEOREM; BINDING SITE; COMPUTER PROGRAM; DNA BINDING; EXPERIMENT; GENE SEQUENCE; GENOME; INTERNET; MAMMAL; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; STATISTICAL MODEL; VALIDATION PROCESS; ALGORITHM; COMPUTER INTERFACE; GENOMICS; METABOLISM; METHODOLOGY; PROBABILITY; REGULATORY SEQUENCE;

MAMMALIA;

ALGORITHMS; BAYES THEOREM; BINDING SITES; GENOMICS; INTERNET; MARKOV CHAINS; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 33747817698     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl212     Document Type: Article

References (22)

1. Fickett,J. and Hatzigeorgiou,A. (1997) Eukaryotic promoter recognition. Genome Res., 7, 861-878.
2. Salzberg,S. (1997) A method for identifying splice sites, translational start sites in eukaryotic mRNA. CABIOS, 13, 365-376.
3. Kel,A.E., Gossling,E., Reuter,I., Cheremushkin,E., Kel-Margoulis,O.V. and Wingender,E. (2003) MATCH™: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
4. Staden,R. (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res., 12, 505-519.
5. Zhang,M.Q. and Marr,T.G. (1993) A weight array method for splicing signal analysis. Comput. Appl. Biosci., 9, 499-509.
6. Barash,Y., Elidan,G., Friedman,N. and Kaplan,T. (2003) Modeling dependencies in protein-dna binding sites. Proceedings of the Annual International Conference on Research in Computational Molecular Biology (RECOMB), 28-37.
7. Benos,P.V., Lapedes,A.S., Fields,D.S. and Stormo,G.D. (2001) Samie: statistical algorithm for modeling interaction energies. In Pacific Symposium on Biocomputing, ACM, NY, pp. 115-126.
8. Bulyk,M.L., Johnson,P.L.F. and Church,G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255-1261.
9. Rissanen,J. (1983) A universal data compression system. IEEE Transactions on Information Theory, 29, 656-664.
10. Ron,D., Singer,Y. and Tishby,N. (1996) The power of amnesia: learning probabilistic automata with variable memory length. Mach. Learn., 25, 117-149.
11. Buhlmann,P. and Wyner,A.J. (1999) Variable length markov chains. Ann. Statist., 27, 480-513.
12. Bejerano,G. and Yona,G. (2001) Variations on probabilistic suffix trees: statistical modeling and prediction of protein families. Bioinformatics, 17, 23-43.
13. Chow,C.K. and Liu,C.N. (1968) Approximating discrete probability distributions with dependence trees. IEEE Transactions on Information Theory, 14, 462-467.
14. Pearl,J. (1988) Probabilistic Reasoning in Intelligent Systems: Networks of plausible inference. Morgan Kaufmann, San Mateo, CA.
15. Buntine,W. (1991) Theory refinement on bayesian networks. In Proceedings of Seventh Conference on Uncertainty in Artificial Intelligence, 52-60, Morgan Kaufmann, Los Angeles, CA.
16. Heckerman,D., Geiger,D. and Chickering,D.M. (1995) Learning bayesian networks. the combination of knowledge and statistical data. Machine Learn., 20, 197-243.
17. Cai,D., Delcher,A., Kao,B. and Kasif,S. (2000) Modeling splice sites with bayes networks. Bioinformatics, 16, 152-158.
18. Castelo,R. and Guigo,R. (2004) Splice site identification by idlbns. Bioinformatics, 20, i69-i76.
19. Ben-Gal,I., Shani,A., Gohr,A., Grau,J., Arviv,S., Shmilovici,A., Posch,S. and Grosse,I. (2005) Identification of transcription factor binding sites with variable-order bayesian networks. Bioinformatics, 21, 2657-2666.
20. Kullback,S. and Leibler,R.A. (1951) On information and sufficiency. Ann. Math. Statist., 22, 79-86.
21. Pruitt,K.D., Tatusova,T. and Maglott,D.R. (2005) Ncbi reference sequence (refseq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res., 33, D501-D504.
22. Wingender,E., Chen,X., Fricke,E., Geffers,R., Hehl,R., Liebich,I., Krull,M., Matys,V., Michael,H., Ohnhäuser,R. et al. (2001) The transfac system on gene expression regulation. Nucleic Acids Res., 29, 281-283.