Weeder web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes

Nucleic Acids Research

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

  Pavesi, Giulio ^a   Mereghetti, Paolo ^b   Mauri, Giancarlo ^b   Pesole, Graziano ^a  

^a UNIVERSITY OF MILAN   (Italy)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; AUTOMATION; BINDING SITE; COMPUTER INTERFACE; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE CONTROL; GENETIC ALGORITHM; GENETIC CONSERVATION; GENETIC PARAMETERS; NONHUMAN; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN MOTIF; STATISTICAL SIGNIFICANCE;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; DNA; GENE EXPRESSION REGULATION; INTERNET; REGULATORY SEQUENCES, NUCLEIC ACID; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 3242884167     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh465     Document Type: Article

References (17)

1. Levine,M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
2. Pavesi,G., Mauri,G. and Pesole,G. (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics, 17 (Suppl. 1), S207-S214.
3. Stormo,G.D. (2000) DNA binding sites: representation and discovery. Bioinformatics, 16, 16-23.
4. Pavesi,G., Mauri,G. and Pesole,G. (2001) Methods for pattern discovery in unaligned biological sequences. Brief. Bioinformatics, 2, 417-430.
5. Berg,O.G. and von Hippel,P.H. (1988) Selection of DNA binding sites by regulatory proteins. Trends Biochem. Sci., 13, 207-211.
6. Frech,K., Quandt,K. and Werner,T. (1997) Finding protein-binding sites in DNA sequences: the next generation. Trends Biochem. Sci., 22, 103-104.
7. Frech,K., Quandt,K. and Werner,T. (1997) Software for the analysis of DNA sequence elements of transcription. Comput. Appl. Biosci., 13, 89-97.
8. Sinha,S. and Tompa,M. (2003) Performance comparison of algorithms for finding transcription factor binding sites, Third IEEE Symposium on Bioinformatics and Bioengineering. Washington DC, pp. 69-78.
9. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
10. 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.
11. Thompson,W., Rouchka,E.C. and Lawrence,C.E. (2003) Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Res., 31, 3580-3585.
12. Marsan,L. and Sagot,M.F. (2000) Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification. J. Comput. Biol., 7, 345-362.
13. Gusfield,D. (1997) Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press, Cambridge, UK and New York.
14. Narasimhan,C., LoCascio,P. and Uberbacher,E. (2003) Background rareness-based iterative multiple sequence alignment algorithm for regulatory element detection. Bioinformatics, 19, 1952-1963.
15. Sinha,S. and Tompa,M. (2002) Discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 30, 5549-5560.
16. Pavesi,G., Mauri,G., Iannelli,F., Gissi,C. and Pesole,G. (2004) GeneSyn: a tool for detecting conserved gene syntenies across genomes. Bioinformatics, 10. 1093/bioinformatics/bth1102
17. Zhu,J and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.