MotifViz: An analysis and visualization tool for motif discovery

Nucleic Acids Research

Volumn 32, Issue WEB SERVER ISS., 2004, Pages

  Fu, Yutao ^a   Frith, Martin C ^a   Haverty, Peter M ^a   Weng, Zhiping ^a,b  

^a BOSTON UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; CYTOSINE; DINUCLEOTIDE; DNA; GUANINE; NUCLEOTIDE; THYMINE;

ACCESS TO INFORMATION; ARTICLE; COMPARATIVE STUDY; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER PROGRAM; DNA SEQUENCE; GENETIC ALGORITHM; INFORMATION PROCESSING; INTERNET; MATHEMATICAL COMPUTING; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; SEQUENCE DATABASE; STATISTICAL ANALYSIS;

ALGORITHMS; BINDING SITES; COMPUTER GRAPHICS; INTERNET; PROMOTER REGIONS (GENETICS); SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EMMELICHTHYS STRUHSAKERI; TRIFOLIUM;

EID: 3242875213     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh426     Document Type: Article

References (17)

1. Lawrence,C.E., Altschul,S.F., Boguski,M.S., Liu,J.S., Neuwald,A.F. and Wootton,J.C. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
2. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
3. Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 296, 1205-1214.
4. Liu,X., Brutlag,D.L. and Liu,J.S. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 127-138.
5. Frith,M.C., Hansen,U., Spouge,J.L. and Weng,Z. (2004) Finding functional sequence elements by multiple local alignment. Nucleic Acids Res., 32, 189-200.
6. Frith,M.C., Fu,Y., Yu,L., Chen,J.F., Hansen,U. and Weng,Z. (2004) Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res., 32, 1372-1381.
7. Liu,R., McEachin,R.C. and States,D.J. (2003) Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Res., 13, 654-661.
8. Sharan,R., Ovcharenko,I., Ben-Hur,A. and Karp,R.M. (2003) CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics, 19(Suppl 1), I283-I291.
9. Elkon,R., Linhart,C., Sharan,R., Shamir,R. and Shiloh,Y. (2003) Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells. Genome Res., 13, 773-780.
10. Aerts,S., Thijs,G., Coessens,B., Staes,M., Moreau,Y. and Moor,B.D. (2003) Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res., 31, 1753-1764.
11. Zheng,J., Wu,J. and Sun,Z. (2003) An approach to identify over-represented cis-elements in related sequences. Nucleic Acids Res., 31, 1995-2005.
12. Haverty,P.M., Hansen,U. and Weng,Z. (2004) Computational inference of transcriptional regulatory networks from expression profiling and transcription factor binding site identification. Nucleic Acids Res., 32, 179-188.
13. Wingender,E., Kel,A.E., Kel,O.V., Karas,H., Heinemeyer,T., Dietze,P., Knuppel,R., Romaschenko,A.G. and Kolchanov,N.A. (1997) TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res., 25, 265-268.
14. Sandelin,A., Alkema,W., Engstrom,P., Wasserman,W.W. and Lenhard,B. (2004) JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res., 32, D91-D94.
15. Berg,O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 723-750.
16. Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
17. Halees,A.S., Leyfer,D. and Weng,Z. (2003) PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res., 31, 3554-3559.