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. 2004 Jul 1;32(Web Server issue):W249-52.
doi: 10.1093/nar/gkh372.

ConSite: web-based prediction of regulatory elements using cross-species comparison

Albin Sandelin  1 , Wyeth W Wasserman, Boris Lenhard
Affiliations

ConSite: web-based prediction of regulatory elements using cross-species comparison

Albin Sandelin et al. Nucleic Acids Res. .

Abstract

ConSite is a user-friendly, web-based tool for finding cis-regulatory elements in genomic sequences. Predictions are based on the integration of binding site prediction generated with high-quality transcription factor models and cross-species comparison filtering (phylogenetic footprinting). By incorporating evolutionary constraints, selectivity is increased by an order of magnitude as compared to single-sequence analysis. ConSite offers several unique features, including an interactive expert system for retrieving orthologous regulatory sequences. Programming modules and biological databases that form the foundation of the ConSite service are freely available to the research community. ConSite is available at http:/www.phylofoot.org/consite.

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Figures

Figure 1
Figure 1
ConSite analysis schema and output formats. Pairs of promoter sequences can either be submitted directly or (for human/mouse) be retrieved by an interactive search (a). Sequences are aligned and analyzed for TFBS using a set of TF models chosen by the user (b). Results can be visualized as a graphical conservation plot (c), as an annotated alignment (d) or in tabular form (e). Individual TFBS and corresponding TF model can be displayed in pop-up windows using sequence logos (f).
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