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PromoterPlot: a graphical display of promoter similarities by pattern recognition

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

In: Nucleic Acids Research, 2005, vol. 33, p. W423-W426

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    Titre
    • PromoterPlot: a graphical display of promoter similarities by pattern recognition
    Auteur
    • Di Cara, Alessandro. Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66, CH-4058 Basel, Switzerland
    • Schmidt, Karsten. Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66, CH-4058 Basel, Switzerland
    • Hemmings, Brian A.. Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66, CH-4058 Basel, Switzerland
    • Oakeley, Edward J.. Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66, CH-4058 Basel, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Nucleic Acids Research, 2005, vol. 33, p. W423-W426. Oxford University Press
    Autre version électronique
    Classification
    • Santé
    Identifiant OAI-PMH
    • oai:doc.rero.ch:289341
    Summary
    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