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]
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]
EcoGene 3.0 a is new web interface for EcoGene.org built using the Drupal open source website software. EcoGene 2.0 and EcoGene both present data from our daily-updated MySql relational database. Some of the scope and content of EcoGene.org will be available only through EcoGene 3.0. EcoGene 2.0 will remain available via a link on the EcoGene 3.0 home page for those who might prefer to continue using it. Please report any problems you find with EcoGene 3.0 to krudd@med.miami.edu. EcoGene-RefSeq is developed to facilitate the usage of EcoGene’s graphic presentations and tools with other genomes. Currently, 2074 complete bacterial genomes from the NCBI RefSeq project are accessible via EcoGene-RefSeq. Cross Reference Mapping and Download is created for user access to many additional accession numbers and other gene identifiers such as gene name, synonyms. GeneSets Venn diagrams GeneSets are collections of genes clustered in EcoTopics, EcoArray or user-provided lists of genes. Venn diagram is an interactive graphic presentation of Boolean query comparisons using or two or three GeneSets. More details are available on the EcoTools page. ... [Information of the supplier]
The Virus Database at University College London has been developed as a system to organize animal virus open reading frame sequences. All known and predicted protein sequences from complete and partial genomes of particular virus families are extracted from GenBank and filtered to remove 100% redundancy. On the basis of sequence similarity the sequences are then clustered into homologous protein families (HPFs). The families are enriched with annotations including function and functional classification, related protein structures, taxonomy, length of the proteins, boundaries of the conserved region/s, virus-specific gene name and links to EMBL entries and SWISSPROT. It is also possible to retrieve the pre-aligned conserved sequence regions or complete protein sequences as fasta format files. Queries can be performed using the family number, virus name, protein function, GenBank identification number or, alternatively, any keyword/s. ... [Information of the supplier]
