1. MatInspector and beyond: promoter analysis based on transcription factor binding sites
- Author
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Kornelie Frech, Korbinian Grote, Thomas Werner, M. Haltmeier, Andreas Klingenhoff, Matthias Frisch, Kerstin Cartharius, M. Bayerlein, and Bernward Klocke
- Subjects
Statistics and Probability ,Transcription, Genetic ,Molecular Sequence Data ,Computational biology ,Biology ,Biochemistry ,Sequence Homology, Nucleic Acid ,Promoter Regions, Genetic ,Molecular Biology ,Gene ,Transcription factor ,Conserved Sequence ,Genetics ,Binding Sites ,Base Sequence ,Promoter ,Promoter analysis ,Sequence Analysis, DNA ,Computer Science Applications ,DNA binding site ,Computational Mathematics ,Computational Theory and Mathematics ,Regulatory sequence ,Sequence Alignment ,Algorithms ,Software ,Protein Binding ,Transcription Factors - Abstract
Motivation: 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. Results: 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). Availability: MatInspector and the other programs described here can be used online at http://www.genomatix.de/matinspector.html. Access is free after registration within certain limitations (e.g. the number of analysis per month is currently limited to 20 analyses of arbitrary sequences). Contact: cartharius@genomatix.de Supplementary information: http://www.genomatix.de/matinspector.html
- Published
- 2005