Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Jul 1;31(13):3593-6.
doi: 10.1093/nar/gkg567.

Regulatory sequence analysis tools

Jacques van Helden  1
Affiliations

Regulatory sequence analysis tools

Jacques van Helden. Nucleic Acids Res. .

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.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Flow chart of the Regulatory Sequence Analysis Tools.
Figure 2
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.
See this image and copyright information in PMC

References

    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. - PubMed
    1. Zhu J. and Zhang,M.Q. (1999) SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607–611. - PubMed
    1. 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. - PMC - PubMed
    1. 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
    1. 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

Publication types

Substances