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]
The Earth Microbiome Project is a proposed massively multidisciplinary effort to analyze microbial communities across the globe. The general premise is to examine microbial communities from their own perspective. Hence we propose to characterize the Earth by environmental parameter space into different biomes and then explore these using samples currently available from researchers across the globe. We will analyze 200,000 samples from these communities using metagenomics, metatranscriptomics and amplicon sequencing to produce a global Gene Atlas describing protein space, environmental metabolic models for each biome, approximately 500,000 reconstructed microbial genomes, a global metabolic model, and a data-analysis portal for visualization of all information. ... [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]
Greenomes provides laboratory and bioinformatics exercises to introduce students to modern plant genetics and genome research. [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]