PRODORIC


34850133	PRODORIC: state-of-the-art database of prokaryotic gene regulation. [PMID: 34850133] Dudek CA, Jahn D. Abstract PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de. Nucleic Acids Res. 2022:50(D1) \| 45 Citations (from Europe PMC, 2025-09-20)
29136200	PRODORIC2: the bacterial gene regulation database in 2018. [PMID: 29136200] Eckweiler D, Dudek CA, Hartlich J, Brötje D, Jahn D. Abstract Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de. Nucleic Acids Res. 2018:46(D1) \| 28 Citations (from Europe PMC, 2025-09-20)
16109747	Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. [PMID: 16109747] Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D. Abstract SUMMARY: 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. AVAILABILITY: http://www.prodoric.de/vfp. Bioinformatics. 2005:21(22) \| 282 Citations (from Europe PMC, 2025-09-20)

PRODORIC: state-of-the-art database of prokaryotic gene regulation. [PMID: 34850133]

Dudek CA, Jahn D.

PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.

Nucleic Acids Res. 2022:50(D1) | 45 Citations (from Europe PMC, 2025-09-20)

PRODORIC2: the bacterial gene regulation database in 2018. [PMID: 29136200]

Eckweiler D, Dudek CA, Hartlich J, Brötje D, Jahn D.

Abstract

Bacteria adapt to changes in their environment via differential gene expression mediated by DNA binding transcriptional regulators. The PRODORIC2 database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database. PRODORIC2 is more intuitive and user-friendly. Besides significant technical improvements, the new update offers more than 1000 new transcription factor binding sites and 110 new position weight matrices for genome-wide pattern searches with the Virtual Footprint tool. Moreover, binding sites deduced from high-throughput experiments were included. Data for 6 new bacterial species including bacteria of the Rhodobacteraceae family were added. Finally, a comprehensive collection of sigma- and transcription factor data for the nosocomial pathogen Clostridium difficile is now part of the database. PRODORIC2 is publicly available at http://www.prodoric2.de.

Nucleic Acids Res. 2018:46(D1) | 28 Citations (from Europe PMC, 2025-09-20)

Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. [PMID: 16109747]

Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D.

Abstract

SUMMARY: 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.
AVAILABILITY: http://www.prodoric.de/vfp.

Bioinformatics. 2005:21(22) | 282 Citations (from Europe PMC, 2025-09-20)

URL:	https://www.prodoric.de/
Full name:
Description:	The PRODORIC database hosts one of the largest collections of DNA binding sites for prokaryotic transcription factors. It is the result of the thoroughly redesigned PRODORIC database.
Year founded:	2005
Last update:	2022-04-19
Version:	1.2.0
Accessibility:	Accessible
Country/Region:	Germany

Data type:	DNA
Data object:	Bacteria
Database category:	Gene genome and annotation
Major species:	Escherichia coli
Keywords:	DNA binding sites transcription factors

University/Institution:	Braunschweig University of Technology
Address:	Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
City:
Province/State:
Country/Region:	Germany
Contact name (PI/Team):	Christian-Alexander Dudek
Contact email (PI/Helpdesk):	c.dudek@tu-braunschweig.de

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Database Commons a catalog of worldwide biological databases