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MatInspector

Search transcription factor binding sites

About Access  
 

MatInspector is our internationally renowned tool for transcription factor analysis. It utilizes MatBase, our comprehensive transcription factor knowledge base, to locate transcription factor binding sites in sequences of unlimited length.

MatInspector is as fast as a search for IUPAC strings but has been shown to produce superior results. It assigns a quality rating to matches (called matrix similarity) and thus allows similarity-based filtering and selection of results. For every single matrix, an individually optimized similarity score is specified, minimizing the number of false positive hits in non-regulatory sequences. Each matrix definition is quality tested, resulting in superior usability for functional analysis of regulatory regions.

The first version of MatInspector is described in Quandt et al., 1995 (NAR). A paper describing all the new features of the current version of MatInspector has recently been published (Cartharius et al., 2005, Bioinformatics).

MatInspector screenshots

What can you do with MatInspector?

  • Search for transcription factor binding sites in a large selection of databases, in any number of database entries or of your own sequences
  • Search in multiple sequences for common TF binding sites
  • Display a graphical representation of the results, and align the matrix sequences
  • Extract sequences for further analysis
  • Alternatively use weight matrices or IUPAC strings as search input
  • Search for individual matrices or for matrix families that group similar and/or functionally related TF binding sites
  • Use both matrix definitions from our database and your own self-defined matrices
  • Use individually optimized, default matrix similarity thresholds, or set your own thresholds
  • Filter vertebrate matrix families according to tissue specificity

Read more in the MatInspector online help.