MatInspector and beyond: promoter analysis based on transcription factor binding sites

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ID: 291035
2005
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Abstract
Promoter analysis is an essential step on the way to identify regulatory networks. A prerequisite for successful promoter analysis is the prediction of potential transcription factor binding sites (TFBS) with reasonable accuracy. The next steps in promoter analysis can be tackled only with reliable predictions, e.g. finding phylogenetically conserved patterns or identifying higher order combinations of sites in promoters of co-regulated genes.We present a new version of the program MatInspector that identifies TFBS in nucleotide sequences using a large library of weight matrices. By introducing a matrix family concept, optimized thresholds, and comparative analysis, the enhanced program produces concise results avoiding redundant and false-positive matches. We describe a number of programs based on MatInspector allowing in-depth promoter analysis (DiAlignTF, FrameWorker) and targeted design of regulatory sequences (SequenceShaper).
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openalex_W2153550523 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Kerstin Cartharius, Kornelie Frech, Korbinian Grote, Bernward Klocke, Manuela Haltmeier, Andreas Klingenhoff, Matthias Frisch, M. Bayerlein, Thomas Werner
Journal BMC Bioinformatics
Year 2005
DOI
10.1093/bioinformatics/bti473
URL
https://academic.oup.com/bioinformatics/article-pdf/21/13/2933/48971040/bioinformatics_21_13_2933.pdf
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