Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes | Zendy

Richard Münch | Zendy; Karsten Hiller | Zendy; Andreas Grote | Zendy; Maurice Scheer | Zendy; Johannes Klein | Zendy; Max Schobert | Zendy; Dieter Jahn | Zendy

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Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes

Author(s) -

Richard Münch,

Karsten Hiller,

Andreas Grote,

Maurice Scheer,

Johannes Klein,

Max Schobert,

Dieter Jahn

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti635

Subject(s) - regulon , visualization , computer science , context (archaeology) , genome , data mining , dna binding site , footprint , computational biology , biology , data science , transcription factor , gene , genetics , promoter , paleontology , gene expression

A new online framework for the accurate and integrative prediction of transcription factor binding sites (TFBSs) in prokaryotes was developed. The system consists of three interconnected modules: (1) The PRODORIC database as a comprehensive data source and extensive collection of TFBSs with corresponding position weight matrices. (2) The pattern matching tool Virtual Footprint for the prediction of genome based regulons and for the analysis of individual promoter regions. (3) The interactive genome browser GBPro for the visualization of TFBS search results in their genomic context and links to gene and regulator-specific information in PRODORIC. The aim of this service is to provide researchers a free and easy to use collection of interconnected tools in the field of molecular microbiology, infection and systems biology.

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