In the field of functional genomics, operon information is often used to observe associations between genomes and biological functions. Genes in an operon are often functionally related hence they appear in the same biological pathway and work together as one system.
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.
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.
A searchable database documenting variation in ribosomal RNA operons in Bacteria and Archaea. The redesigned rrnDB brings a substantial increase in the number of genomes described, improved curation, mapping of genomes to both NCBI and RDP taxonomies, and refined tools for querying and analyzing these data. With these changes, the rrnDB is better positioned to remain a comprehensive resource under the torrent of microbial genome sequencing.
Consists of an online resource of predicted operons in microbial genomes. OperonDB contains details concerning over 550 bacterial and archaeal genomes, comprising the complete collection of finished prokaryotic genomes available from Genbank. Moreover, it offers users a method to detect and analyze conserved gene pairs - pairs of genes that are located close on the same DNA strand in two or more bacterial genomes.
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.
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.
Collects regulatory information about S. oneidensis MR-1. Shewregdb is a curated database that compiles the basic regulatory entities, their characteristics and main types of the regulatory elements derived from a computational prediction gathered from published experimental data. Users can visualize the results using a GB browser. Searches can be made by DNA regulator binding sites, RNA regulators and operons.