A database is a model of a piece of the world. RegulonDB in this sense is a model of the complex regulation of transcription initiation or regulatory network of the cell, on the one hand. On the other hand, it is also a model of the organization of the genes in transcription units, operons and simple and complex regulons. In this sense, RegulonDB is a computational model of mechanisms of transcriptional regulation. ... [Information of the supplier]
Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. ... [Information of the supplier]
This server is constructed around a database dedicated to the analysis of the genome of Escherichia coli: Colibri. Its purpose is to collate and integrate various aspects of the genomic information from E. coli, the paradigm of Gram-negative bacteria. Colibri provides a complete dataset of DNA and protein sequences derived from the paradigm strain E. coli K-12, linked to the relevant annotations and functional assignments. It allows one to easily browse through these data and retrieve information, using various criteria (gene names, location, keywords, etc.). ... [Information of the supplier]
CyBib is a bibliographic database exclusively for scientific literature about cyanobacteria (blue-green algae). The entire database has been parked on the Internet to provide a resource for researchers and students involved with cyanobacteria. CyBib v5 is the seventh generation of the database to be presented on the Internet. It contains nearly 25,000 references. These references were collected in large part by Jeff Elhai, known for his Internet outreach work as the founder, editor, and publisher of CyanoNews. The other contributors are too numerous to name. ... [Information of the supplier]
DOLOP provides information for several hundred lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins ... [Information of the supplier, modified]
The Ribosomal Database Project (RDP) provides ribosome related data services to the scientific community, including online data analysis, rRNA derived phylogenetic trees, and aligned and annotated rRNA sequences. [Information of the supplier]
The goal of creating the Human Oral Microbiome Database (HOMD) is to provide the scientific community with comprehensive information on the approximately 600 prokaryote species that are present in the human oral cavity. The majority of these species are uncultivated and unnamed, recognized primarily by their 16S rRNA sequences. The HOMD presents a provisional naming scheme for the currently unnamed species so that strain, clone, and probe data from any laboratory can be directly linked to a stably named reference entity. The HOMD links sequence data with phenotypic, phylogenetic, clinical, and bibliographic information. Full and partial oral bacterial genome sequences determined as part of this project and the Human Microbiome Project, are being added to the HOMD as they become available. HOMD offers easy to used tools for viewing all publically available oral bacterial genomes. ... [Information of the supplier]
Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. ICEs are self-transmissible elements that encode a full complement of machinery for conjugation as well as intricate regulatory systems to control excision from the chromosome and onward conjugative transfer [Wozniak and Waldor, 2010; Burrus,2004]. These multi-talented entities can promote their own mobilization and potentially that of other 'hitch-hiking' genetic elements and thus contribute to horizontal transfer of virulence determinants, antibiotic-resistance genes and other bacterial traits [Hastings. et al., 2004]. ICEs are being identified in increasing numbers as sequenced genome databases expand exponentially [Wozniak, et al., 2010; Ryan, et al., 2009; te Poele, et al., 2008; Burrus et al., 2002]. At present only a few have been classified into ICE families, amongst the best characterized of which is the SXT/R391 family of Vibrio cholerae, like SXT of Vibrio cholerae O139 MO10. In addition, several elements discovered more than a decade ago which had previously been classified as plasmids or conjugative transposons, such as pSAM2 and Tn916 , have now been defined as ICEs. ICEs typically exhibit a number of features that are of interest to researchers in the fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. These include high levels of functional diversity, foreign and frequently patchwork origins and sparse experimental data on these entities. We are collating available experimental and bioinformatics analyses data and literature about known and putative ICEs in bacteria as a PostgreSQL-based database called ICEberg. As its name implies we expect that ICEberg will continue to grow from its currently visible tiny 'tip' representing presently known ICEs to a very substantial database as more and more of these entities are revealed. ... [Information of the supplier]
Database of Bacterial ExoToxins for Human (DBETH) is a database of sequences, structures, interaction networks and analytical results for 229 exotoxins, from 26 different human pathogenic bacterial genus. All toxins are classified into 24 different Toxin classes. The aim of DBETH is to provide a comprehensive database for human pathogenic bacterial exotoxins. DBETH also provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach). ... [Information of the supplier]
In 2001 a suite of legacy databases relating to mycology, bacteriology, systematics and pathology were consolidated into an integrated information resource and some (but not all) of these data, were made available through the NZFUNGI website. The development of NZFUNGI was one output from the Database Integration Project (DIP) which ran from 1999-2004 and was partly funded by the Foundation for Research Science and Technology. DIP was focussed on redevelopment and accessibility of the data contained in the seven FRST Nationally Significant Databases & Collections maintained by Landcare Research. The National Fungal Herbarium (PDD) and the International Collection of Micro-organisms from Plants (ICMP) are two of those collections/databases, and the data from the dried and living collections of fungi and bacteria form one part of the NZFUNGI information resource. ... [Information of the supplier]