MatInspector
Introduction
MatInspector is the internationally renowned tool for transcription factor analysis. It utilises MatBase, the comprehensive transcription factor knowledge base, to locate transcription factor binding sites in sequences of unlimited length.
MatInspector is a software tool that utilises a large library of matrix descriptions for transcription factor binding sites to locate matches in DNA sequences. MatInspector is almost as fast as a search for IUPAC strings but has been shown to produce superior results. It assigns a quality rating to matches and thus allows quality-based filtering and selection of matches.
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 optimised similarity score is specified, minimising 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.
Features
- Similar and/or functionally related transcription factor binding sites are grouped into so-called matrix families
- Individually optimised default matrix similarity thresholds for all matrices
- User-defined IUPAC strings and predefined IUPAC libraries can be used
- Graphical representation of the results
- Search several different sequences for common TF sites
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 optimised, default matrix similarity thresholds, or set your own thresholds
- Filter vertebrate matrix families according to tissue specificity