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Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences

Nature Protocols volume 3, pages 1589–1603 (2008)Cite this article

Abstract

This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription factor-binding motifs in promoters of coregulated genes and (ii) discovering phylogenetic footprints in promoters of orthologous genes. The steps of this protocol include purging genomic sequences to discard redundant fragments, discovering over-represented patterns and assembling them to obtain degenerate motifs, scanning sequences and drawing feature maps. The main strength of the method is its statistical ground: the binomial significance provides an efficient control on the rate of false positives. In contrast with optimization-based pattern discovery algorithms, the method supports the detection of under- as well as over-represented motifs. Computation times vary from seconds (gene clusters) to minutes (whole genomes). The execution of the whole protocol should take ∼1 h.

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Figure 1
Figure 2: The Web interface of oligo-analysis is divided in five sections separated by dashed lines.
Figure 3: Example of pattern discovery in promoters bound by the transcription factor Spo0A from Bacillus subtilis.
Figure 4: Comparison between oligo-analysis and dyad-analysis for the FNR regulon.
Figure 5: Example of pattern discovery in promoters of orthologous genes.
Figure 6: Detection of restriction sites in whole genomes.

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Acknowledgements

This work was supported by the Belgian Program on Interuniversity Attraction Poles, initiated by the Belgian Federal Science Policy Office, project P6/25 (BioMaGNet), by the BioSapiens Network of Excellence funded under the sixth Framework program of the European Communities (LSHG-CT-2003-503265) and by the Fonds pour la Formation à la Recherche dans l'Industrie et dans l'Agriculture, FRIA (R.J. PhD grant). We acknowledge the students of the Licenciatura en Ciencias Genomicas (CCG-UNAM, Mexico) and the Instituto de Biotecnologia (IBT-UNAM, Mexico) for having tested the protocol and provided useful feedback.

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  1. Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe), Université Libre de Bruxelles, Campus Plaine, CP 263, Boulevard du Triomphe, Bruxelles, B-1050, Belgium

    Matthieu Defrance, Rekin's Janky, Olivier Sand & Jacques van Helden

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  1. Matthieu Defrance
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Correspondence to Jacques van Helden.

Supplementary information

Supplementary Fig. 1

Feature-map of the significant oligonucleotides. Note that the precise values of the oligo-analysis results can slightly vary with successive versions of the genome stored at NCBI. (PDF 116 kb)

Supplementary Fig. 2

Feature-maps of the significant dyads detected in purE promoters of Enterobacteriales (PDF 58 kb)

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Defrance, M., Janky, R., Sand, O. et al. Using RSAT oligo-analysis and dyad-analysis tools to discover regulatory signals in nucleic sequences. Nat Protoc 3, 1589–1603 (2008). https://doi.org/10.1038/nprot.2008.98

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