CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels, Class(C), Architecture(A), Topology(T) and Homologous superfamily (H).Class, derived from secondary structure content, is assigned for more than 90% of protein structures automatically. Architecture, which describes the gross orientation of secondary structures, independent of connectivities, is currently assigned manually. The topology level clusters structures into fold groups according to their topological connections and numbers of secondary structures. The homologous superfamilies cluster proteins with highly similar structures and functions. The assignments of structures to fold groups and homologous superfamilies are made by sequence and structure comparisons. The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures. These include computational techniques, empirical and statistical evidence, literature review and expert analysis. ... [Information of the supplier]
Codon Usage Database is an extended WWW version of CUTG (Codon Usage Tabulated from GenBank). The frequency of codon use in each organism is made searchable through this World Wide Web site. Data amount: 32,775 organisms, 2,298,913 complete protein coding genes (CDS's), as of January 2007. Usage: A query box to search a codon usage table for an organism, is presented. Search can be done with Latin name or its sub-string of organism. ... [Information of the supplier]
The Consortium for the Barcode of Life (CBOL) is an international initiative devoted to developing DNA barcoding as a global standard in taxonomy. CBOL has more than 130 Member Organizations from 40 countries. DNA Barcoding is a technique that uses a short gene sequence from a standardized region of the genome as a diagnostic “biomarker” for species. Different species have different DNA barcodes, making it possible to use barcodes to: (1) identify specimens, (2) discover possible new species, and (3) to make taxonomy more effective for science and society. ... [Information of the supplier]
Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. ... [Information of the supplier]
Welcome to DAVID Bioinformatics Resources 2003 – 2009. The Database for Annotation, Visualization and Integrated Discovery (DAVID). DAVID 2008 is the sixth version of our original web-accessible programs. DAVID now provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes. For any given gene list, DAVID tools are able to identify enriched biological themes, particularly GO terms; to discover enriched functional-related gene groups; to search for other functionally related genes; to list interacting proteins; and to link gene-disease associations. ... [Information of the supplier, modified]
Dendrome is a collection of forest tree genome databases and other forest genetic information resources for the international forest genetics community. Dendrome is part of a larger collaborative effort to construct genome databases for major crop and forest species. [Information of the supplier]
The Dfam database is a collection of Repetitive DNA element sequence alignments, hidden Markov models (HMMs) and matches lists for complete Eukaryote genomes. Transposable elements (or interspersed repeats) account for a substantial portion of eukaryotic genomes. Accurate annotation of TEs enables research into their biology and can shed light on the evolutionary processes that shape genomes. Dfam represents a collection of alignments and HMMs of such transposable elements and other repetitive DNA elements. The Dfam website gives information about each model, and provides genome annotations for a collection of core genomes. The models may also be downloaded from the ftp site, for example to mask repeats in new genomes. ... [Information of the supplier]
The DNA Bank Network was established in spring 2007 and is currently funded by the German Science Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility). It offers a worldwide unique concept. DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals). ... [Information of the supplier]
DDBJ (DNA Data Bank of Japan) began DNA data bank activities in earnest in 1986 at the National Institute of Genetics (NIG). From the beginning, DDBJ has been functioning as one of the International DNA Databases, including EBI in Europe and NCBI in the USA as the two other members. Consequently, we have been collaborating with the two data banks through exchanging data and information on Internet and by regularly holding two meetings, the International DNA Data Banks Advisory Meeting and the International DNA Data Banks Collaborative Meeting. DDBJ is the sole DNA data bank in Japan, which is officially certified to collect DNA sequences from researchers and to issue the internationally recognized accession number to data submitters. We collect data mainly from Japanese researchers, but of course accept data and issue the accession number to researchers in any other countries. Since we exchange the collected data with EMBL/EBI and GenBank/NCBI on a daily basis, the three data banks share virtually the same data at any given time. We also provide worldwide many tools for data retrieval and analysis developed by at DDBJ and others. ... [Information of the supplier]