MATCH: A tool for searching transcription factor binding sites in DNA sequences. Match is a weight matrix-based tool for searching putative transcription factor binding sites in DNA sequences. Match is closely interconnected and distributed together with the TRANSFAC database. In particular, Match uses the matrix library collected in TRANSFAC and therefore provides the possibility to search for a great variety of different transcription factor binding sites. Several sets of optimised matrix cut-off values are built in the system to provide a variety of search modes of different stringency. The user may construct and save his/her specific user profiles which are selected subsets of matrices including default or user-defined cut-off values. Furthermore a number of tissue-specific profiles are provided that were compiled by the TRANSFAC team. A public version of the Match tool is available at: The same program with a different web interface can be found at An advanced version of the tool called Match Professional is available at

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  1. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  2. Pizzi, Cinzia; Ukkonen, Esko: Fast profile matching algorithms - A survey (2008)
  3. Levitsky, Victor G.; Ignatieva, Elena V.; Ananko, Elena A.; Turnaev, Igor I.; Merkulova, Tatyana I.; Kolchanov, Nikolay A.; Hodgman, T. C.: Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions (2007) ioport
  4. Stepanova, Maria; Lin, Geng; Lin, Valerie C.-L.: Establishing a statistic model for recognition of steroid hormone response elements (2006)
  5. Haverty, Peter M.; Weng, Zhi-Ping; Hansen, Ulla: Transcriptional regulatory networks activated by PI3K and ERK transduced growth signals in human glioblastoma cells (2005) ioport