The MicrobesOnline genome database contains over 300 prokaryotic genomes. All genomes are automatically analyzed through the VIMSS genome pipeline. We use publicly available sequence analysis tools and databases to search for homologs (NCBI BLAST, SwissProt, COG) and protein domains (InterPro), to assign gene ontologies (Gene Ontology Consortium) and EC numbers and to map the metabolic pathways (KEGG). We then link the orthology relationships between genes, predict operon structures and regulon networks. Most of the genomes are downloaded from NCBI and genes are parsed from GenBank files. When an incomplete genome is directly downloaded from a sequencing center, we predict protein coding genes using CRITICA and Glimmer, tRNA genes using tRNAscan and other RNA genes by BLASTn. All of the info in the VIMSS genome database is freely available on our website. ... [Information of the supplier]
The German Society for Mycology (DGfM) heralded a new era in the occurrence registration of macrofungi with the project “Ecological Fungus Mapping 2000”. This does not replace the, up to the present, chorological mapping whose results, 4 million records of occurrence gathered over 18 years of painstaking work by the former President of the DGfM German Krieglsteiner, are immortalised in 2 volumes of the “Distribution Atlas of German Macrofungi”. “Mapping 2000” is rather to be understood as an extension of pure chorological mapping. The computer support with the PC program “Ecological Fungus Mapping 2000” makes it possible to evaluate and administer records. The DGfM thus expects from the same co-worker activity a 15-times increase in the data. [Deutsche Gesellschaft für Mykologie - translation: vifabio] ... [Miscellaneous as indicated]
PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete and bacterial pathogens, which infect animal, plant, fungal and insect hosts. PHI-base is therfore an invaluable resource in the discovery of genes in medically and agronomically important pathogens, which may be potential targets for chemical intervention. In collaboration with the FRAC team, PHI-base also includes antifungal compounds and their target genes. Each entry in PHI-base is curated by domain experts and is supported by strong experimental evidence (gene disruption experiments, STM etc), as well as literature references in which the original experiments are described. Each gene in PHI-base is presented with its nucleotide and deduced amino acid sequence, as well as a detailed description of the predicted protein's function during the host infection process. To facilitate data interoperability, we have annotated genes using controlled vocabularies and links to external sources. ... [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]
xBASE is a database for comparative genome analysis of all bacterial genome sequences, with particular emphasis on organisms of significance to AgriFood. The project was originally conceived in 2002 by Roy Chaudhuri and Mark Pallen at the University of Birmingham, as part of a BBSRC funded Exploiting Genomics (ExGen) consortium. ... [Information of the supplier]
Culture Collections Information Worldwide is a database management system for culture collections in the world. It includes CCINFO and STRAIN. CCINFO is a world directory of all registered culture collections. The database STRAIN includes list of holdings from registered culture collections. [Information of the supplier]
ProGlycProt (Prokaryotic Glycoproteins) is a manually curated, comprehensive repository of experimentally characterized bacterial glycoproteins and archaeal glycoproteins, generated from an exhaustive literature search. This is the focused beginning of an effort to provide concise relevant information derived from rapidly expanding literature on prokaryotic glycoproteins, their glycosylating enzyme(s), glycosylation linked genes, and genomic context thereof, in a cross-referenced manner. ProGlycProt is an extensive online collection of experimentally verified glycosites and glycoproteins of the prokaryotes. For users’ benefit, the database under menu ProGlycProtdb is arranged into two sections namely, ProCGP and ProUGP. ProCGP is the main section containing characterized prokaryotic glycoproteins, defined as entries with at least one experimentally known "glycosylated residue (glycosite)". Whereas, ProUGP is the supplementary section, presenting uncharacterized prokaryotic glycoproteins, defined as entries with experimentally identified glycosylation but unidentified glycosites. The ProGlycProt has been developed with an aim to aid and advance the emerging scientific interests in understanding the mechanisms, implications, and novelties of protein glycosylation in prokaryotes that include many pathogenic as well as economically important bacterial species. A general data update policy is once in three months. Existing entries are updated in real-time. ... [Information of the supplier]
The degradation of xenobiotic and other toxic compounds by microorganisms is central to strategies for the bioremediation of contaminated environments. The Center for Microbial Ecology at Michigan State University and Rutgers University initiated a study to establish the phylogenetic distribution of described, biodegrading microorganisms with the goals of identifying patterns of microbial degradative processes within a phylogenetic context and of gaining insights into the evolution of those processes. This continuing investigation has been hindered by strain data that is difficult to comprehensively compile and often uncomparable between strains and has underscored the potential usefulness of a database that would consolidate strain-level microbial data. To address this need and provide a resource for the scientific community, we have developed the Biodegradative Strain Database (BSD). The BSD is being developed at the Center for Microbial Ecology in collaboration with the University of Minnesota Biocatalysis/Biodegradation Database and the Ribosomal Database Project II . It should consolidate and provide rapid access to comparative data on known biodegradative microorganisms and the hazardous substances they degrade as a readily accessible resource for researchers and field practitioners. One of its other goals is to facilitate comparative analyses and highlight deficiencies in our current knowledge base. ... [Information of the supplier, modified]
