The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources. ... [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]
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 SOL Genomics Network (SGN) is a clade oriented database dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida. SGN is part of the International Solanaceae Initiative (SOL), which has the long-term goal of creating a network of resources and information to address key questions in plant adaptation and diversification. A key problem of the post-genomic era is the linking of the phenome to the genome, and SGN allows to track and help discover new such linkages. ... [Information of the supplier]
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 SoyBase web presence offers a comprehensive spectrum of data and tools for research on the soya bean, Glycine max. It integrates genetic and molecular-biological resources that are particularly relevant to the use of the soya bean. The data are organised primarily in the form of maps (Genetic Map, Physical Map, Sequence Map). ... [Editorial staff vifabio]
Greenomes provides laboratory and bioinformatics exercises to introduce students to modern plant genetics and genome research. [Information of the supplier]
The CGP is a resource for the Compositae, one of the largest and ecologically successful families. Lettuce is one of the top ten US crops and sunflower ranks #14 worldwide. The Compositae also includes many minor crops, important weeds, and species with novel biochemistries. The CGP transitions basic genomics information to crop improvement by leveraging information from the sequencing and functional genomics of model organisms. In turn, it will contribute data to the synthetic information being developed across all plants. ... [Information of the supplier, modified]
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]
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]
