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Nucleic Acids Research 2005 33(Web Server Issue):W423-W426; doi:10.1093/nar/gki413
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

PromoterPlot: a graphical display of promoter similarities by pattern recognition

Alessandro Di Cara, Karsten Schmidt, Brian A. Hemmings and Edward J. Oakeley*

Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66, CH-4058 Basel, Switzerland

*To whom correspondence should be addressed. Tel: +41 61 697 6986; Fax: +41 61 697 3976; Email: edward.oakeley{at}fmi.ch

Received February 22, 2005. Revised March 21, 2005. Accepted March 21, 2005.

PromoterPlot (http://promoterplot.fmi.ch) is a web-based tool for simplifying the display and processing of transcription factor searches using either the commercial or free TransFac distributions. The input sequence is a TransFac search (public version) or FASTA/Affymetrix IDs (local install). It uses an intuitive pattern recognition algorithm for finding similarities between groups of promoters by dividing transcription factor predictions into conserved triplet models. To minimize the number of false-positive models, it can optionally exclude factors that are known to be unexpressed or inactive in the cells being studied based on microarray or proteomic expression data. The program will also estimate the likelihood of finding a pattern by chance based on the frequency observed in a control set of mammalian promoters we obtained from Genomatix. The results are stored as an interactive SVG web page on our server.

Present address: Karsten Schmidt, The Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA


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