CGD is an organized collection of genetic and molecular biological information about Candida albicans, a yeast that is an opportunistic pathogen of humans. It contains information about Candida albicans genes and proteins; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information. The CGD Home page is the main entry point for the database. CGD is aimed at scientists; collected information for the non-scientist about Candida albicans and other yeasts can be found at the Yeast Virtual Library. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health. ... [Information of the supplier]
The CATMA database is publicly and freely available. The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments. CATMA microarrays constitute the foundation of the CAGE project aiming at the construction of a gene expression reference database for Arabidopsis. The CATMA GSTs are also the basic materials in the AGRIKOLA project focusing on the large-scale systematic RNAi silencing of Arabidopsis genes. CATMA is a consortium of research groups from eight European countries. All CATMA members are public laboratories, some with ties to private research institutions. In the years 2001 to 2003, they contributed to the purchase of the reagents and to the work necessary for the production of the version 1 (v1) and v2 GST repertoires. A synchronization of the repertoire in 2005 with the at that time latest Arabidopsis genome annotations (TIGR5 and Eugène040917)lead -with financial support of the French, German, Swedish, Swiss, UK and Belgian members- to repertoire v3 containing 30,343 GSTs. A last design effort was undertaken in 2006 by the Swiss consortium member, in which an extra 543 GSTs could be designed by using less stringent design criteria, thus forming repertoire v4. Probes were now also allowed to simultaneously tag multiple members of gene families, leading to 990 GFTs (Gene Family Tags). The description of these GFTs can be found on the CATMA Gene Family Tag website. ... [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]
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. ... [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]
Estimation of nuclear DNA content is the most frequent application of flow cytometry in plants. The growing number of publications in this field calls for an efficient tool to access and analyze the published information. The FLOWer database is a unique resource that lists all publications on DNA flow cytometry and enables their quantitative evaluation. Unbiased data can be obtained on taxonomic groups that were analysed, the use of nuclear isolation buffers and methods of standardization, including DNA reference standards, the use of fluorochromes and measures of result quality. The objective(s) of individual studies can be assessed as well as the flow cytometers that were used, scientific journals in which the results were published and countries of author's origin. ... [Information of the supplier]
FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. In its first iteration (released in early 2011), FungiDB contains the genomes of 18 Fungi covering 17 species. FungiDB integrates whole genome sequence and annotation and will expand to include experimental data and environmental isolate sequences provided by the community of researchers. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining. ... [Information of the supplier]
Funded as part of the Wellcome Trust Functional Genomics Development Initiative, the GeneDB project is aiming to develop and maintain curated database resources for three organisms: Schizosaccharomyces pombe, which has been completely sequenced, and the kinetoplastid protozoa Leishmania major and Trypanosoma brucei, whose genome sequences have yet to be completed. The goals are to capture, store and manage data for integration with emerging functional genomics and proteomics projects and to provide an easy-to-use, user-friendly interface, including a variety of graphical displays. It is envisaged that the generic database structure will subsequently be adopted to integrate datasets for other organisms, both prokaryotic and eukaryotic, that have been sequenced by the Sanger Institute Pathogen Sequencing Unit. To this extend, datasets for Saccharomyces cerevisiae as well as the filamentous fungus Aspergillus fumigatus are already available through GeneDB. The database has been developed through close collaboration between Sanger Institute software developers, on-site organism specific curators and representatives of the research communities. The data within geneDB are manually annotated and curated, frequently updated and, because of the structured annotation and use of controlled vocabulary, easy to precisely query. The database is under constant review and new functionality will be added as it evolves. ... [Information of the supplier]
The rice genome is more than a resource for understanding the biology of a single species. It is a window into the structure and function of genes in other crop grasses as well. Using rice as the sequenced reference genome, researchers can identify and understand the relationships among genes, pathways and phenotypes in a wide range of grass species.Extensive work over the past two decades has shown remarkably consistent conservation of gene order within large segments of linkage groups in rice, maize, sorghum, barley, wheat, rye, sugarcane and other agriculturally important grasses. A substantial body of data supports the notion that the rice genome is substantially colinear at both large and short scales with other crop grasses, opening the possibility of using rice synteny relationships to rapidly isolate and characterize homologues in maize, wheat, barley and sorghum. As an information resource, Gramene's purpose is to provide added value to data sets available within the public sector, which will facilitate researchers' ability to understand the rice genome and leverage the rice genomic sequence for identifying and understanding corresponding genes, pathways and phenotypes in other crop grasses. This is achieved by building automated and curated relationships between rice and other cereals for both sequence and biology. ... [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]
