Regulatory sequence analysis tools - PubMed (original) (raw)
Regulatory sequence analysis tools
Jacques van Helden. Nucleic Acids Res. 2003.
Abstract
The web resource Regulatory Sequence Analysis Tools (RSAT) (http://rsat.ulb.ac.be/rsat) offers a collection of software tools dedicated to the prediction of regulatory sites in non-coding DNA sequences. These tools include sequence retrieval, pattern discovery, pattern matching, genome-scale pattern matching, feature-map drawing, random sequence generation and other utilities. Alternative formats are supported for the representation of regulatory motifs (strings or position-specific scoring matrices) and several algorithms are proposed for pattern discovery. RSAT currently holds >100 fully sequenced genomes and these data are regularly updated from GenBank.
Figures
Figure 1
Flow chart of the Regulatory Sequence Analysis Tools.
Figure 2
Feature map of the patterns discovered in Table 2. Each box corresponds to one hexanucleotide. Transcription factor binding sites are generally revealed as combinations of boxes, which reflect the fact that the consensus is >6 nt. The blue box corresponds to CACGTG, the core of Met4p binding site. Some examples of the smaller boxes, corresponding to putative Met31p binding sites, are indicated. Notice that putative Met31p binding sites are often associated to putative Met4p binding sites, suggesting an interaction between the two factors.
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References
- 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. - PubMed
- Zhu J. and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607–611. - PubMed
- 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. - PMC - PubMed
- 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. - PubMed
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