BEST: Binding-site Estimation Suite of Tools

Bioinformatics

Volumn 21, Issue 12, 2005, Pages 2909-2911

  Che, Dongsheng ^a   Jensen, Shane ^b   Cai, Liming ^a   Liu, Jun S ^c  

^a University of Georgia ^*  (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; AUTOMATION; BINDING SITE; COMPUTER PROGRAM; COMPUTER SYSTEM; CONSENSUS; DNA BINDING MOTIF; INTERNET; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN MOTIF;

EID: 20844455471     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti425     Document Type: Article

References (13)

1. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, Stanford, CA. AAAI Press, Bethesda, MD, pp. 28-36.
2. Galas,D.J. and Schmitz,A. (1978) A DNA footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res., 5, 3157-3170.
3. Garner,M.M. and Revzin,A. (1981) A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res., 9, 3047-3060.
4. Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
5. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
6. Jensen,S.T. and Liu,J.S. (2004) BioOptimizer: a Bayesian scoring function approach to motif discovery. Bioinformatics, 20, 1557-1564.
7. Jensen,S.T. et al. (2004) Computational discovery of regulatory binding motifs: a Bayesian perspective. Statist. Sci., 19, 188-204.
8. Lawrence,C.E. et al. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
9. Liu,J.S. et al. (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Am. Statist. Assoc., 90, 1156-1170.
10. Liu,X. et al. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 6, 127-138.
11. Liu,X. et al. (2002) An algorithm for finding protein-DNA interaction sites with applications to chromatin immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
12. Olman,V. et al. (2003) CUBIC: identification of regulatory binding sites through data clustering. J. Bioinform. Computat. Biol., 1, 21-40.
13. Roth,F.R. et al. (1998) Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.