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DOOR / Database of prOkaryotic OpeRons
Contains computationally predicted operons of all the sequenced prokaryotic genomes. DOOR provides the following tools: (i) a predictor for transcriptional units (Tus), (ii) a computer program for mapping orthologous genes across genomes, (iii) a search capability enabling to retrieve information stored in the database, (iv) operon predictors and (v) a genome browser to support visualization of selected operons along with TU structures under multiple conditions. It is usually used for prediction or retrieval for operons involved in virulence or regulation.
ProOpDB / Prokaryotic Operon DataBase
Constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: (i) organism name, (ii) metabolic pathways, as defined by the KEGG database, (iii) gene orthology, as defined by the COG database, (iv) conserved protein domains, as defined by the Pfam database, (v) reference gene and (vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient method to select the most representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool to visualize their genomic context and retrieve the sequence of their corresponding 5' regulatory regions, as well as the nucleotide or amino acid sequences of their genes.
ODB / Operon DataBase
Aims to collect known and conserved operons in multiple species. All the known operons are derived from the literature and from publicly available database including operon information. We will collect as many operons (transcriptional units) as possible from as many organisms as possible. As for the concept of reference operons, our system provides candidates of operons based on the orthologous genes conserved in the genomes. This database integrates both known literature-based operons as well as predicted well-conserved operons, to provide a useful system for bioinformatics researchers and experimental biologists.
MycoperonDB
Provides literature links for experimentally characterized operons. MycoperonDB is a database of computationally predicted operons and transcriptional units of Mycobacteria. All known promoters and related information is collected, analysed and stored. This database provides a user-friendly interface to allow a web based navigation of transcription units and operons. The web interface provides search tools to locate transcription factor binding DNA motif upstream to various genes.
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