Regulatory Sequence Analysis Tools

Nucleic Acids Research

Volumn 31, Issue 13, 2003, Pages 3593-3596

  van Helden, Jacques ^a  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; GENBANK; GENE SEQUENCE; GENETIC CODE; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERNET; PREDICTION; PRIORITY JOURNAL; REGULATORY SEQUENCE; SEQUENCE ANALYSIS; BINDING SITE; COMPUTER GRAPHICS; COMPUTER INTERFACE; DNA FLANKING REGION; GENOME; METABOLISM; METHODOLOGY;

TRANSCRIPTION FACTOR;

5' FLANKING REGION; ALGORITHMS; BINDING SITES; COMPUTER GRAPHICS; GENOME; INTERNET; REGULATORY SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 0041620271     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg567     Document Type: Article

References (10)

1. van Helden,J., Andre,B. and Collado-Vides,J. (2000) A web site for the computational analysis of yeast regulatory sequences. Yeast, 16, 177-187.
2. Zhu,J. and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
3. Matys,V. Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
4. Salgado,H., Santos-Zavaleta,A., Gama-Castro,S., Millan-Zarate,D., Diaz-Peredo,E., Sanchez-Solano,F., Perez-Rueda,E., Bonavides-Martinez,C. and Collado-Vides,J. (2001) RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res., 29, 72-74.
5. Hertz,G.Z., Hartzell,G.W.d. and Stormo,G.D. (1990) Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci., 6, 81-92.
6. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
7. van Helden,J., Andre,B. and Collado-Vides,J. (1998) Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
8. van Helden,J., Rios,A.F. and Collado-Vides,J. (2000) Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res., 28, 1808-1818.
9. Neuwald,A.F., Liu,J.S. and Lawrence,C.E. (1995) Gibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci., 4, 1618-1632.
10. van Helden,J. (2003) Prediction of transcriptional regulation by analysis of the non-coding genome. Curr. Genomics, 4, 217-224.