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Bgee is a database to compare expression patterns between animal species. Bgee addresses difficulties such as complex anatomies and diverse sources of data by the use of ontologies and the explicit representation of homology. Homology relationships are defined both between genes and between anatomical features. The main efforts are the annotation of anatomical and developmental terms and their homology relationships, and the annotation and statistical treatment of transcriptome data.
keywords: anatomy, embryonic development, EST, evolution, expression, homology, in situ hybridization, microarray
ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.
GlycoSuiteDB is a curated and annotated glycan database
GPSDB (Gene and Protein Synonym DataBase) collects gene/protein names, in a species specific way, from several biological resources. A web-based search interface gives access to the database: given a gene/protein name, it retrieves all synonyms for this entity and queries Medline with a set of user-selected terms.
A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.
MIAPEGelDB helps end-users to write MIAPE documents (minimum information to report when describing or publishing a proteomics experiment), through a self-documenting web interface. The produced documents are stored in a database, and thus remain easily accessible by anybody through a stable URL unique for each document.
keywords: gel electrophoresis, protocol
miROrtho contains predictions of precursor miRNA genes covering many animal genomes combining evidence from sequence homology and Support Vector Machine classifiers. We provide both consistent extrapolation of already known miRBase families and novel miRNA predictions by our SVM and orthology pipeline.
neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools.
The OpenFlu database (OpenFluDB) is part of a collaborative effort to share observations on the evolution of Influenza virus in both animals and humans. It contains genomic and protein sequences as well as epidemiological data from more than 25'000 isolates.
OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny. Available protein descriptors, together with Gene Ontology and InterPro attributes, serve to provide general descriptive annotations of the orthologous groups, and facilitate comprehensive database querying.
keywords: animal, arthropod, evolution, evolutionary relation, family database, functional annotation, fungi, genomics, homology, human, insect, orthology, paralogy, protein characterization, protein database, protein family, protein function, proteome database, sequence characterisation, sequence retrieval, vertebrate
Along with sequence data for Pfam gene families and protein domains, PANDITplus provides access to data on protein interactions, functional and chemical pathway annotation, gene expression, and association with disease, and pre-computed estimates from evolutionary codon models.
PaxDb contains estimated abundance values for a large number of proteins in several different species (12 in version 2.0). Furthermore, it contains information about inter-species variation of protein abundances.
Publication électronique (en français) de vulgarisation scientifique du groupe Swiss-Prot de l'Institut Suisse de Bioinformatique dédiée aux protéines qui font parler d'elles dans l'actualité.
PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them.
Protein Spotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone.
Selectome is a database of positive selection based on a rigorous branch-site specific likelihood test. Positive selection is detected using CODEML on all branches of animal gene trees. The web interface of Selectome enables queries according both to the results of positive selection tests, and to gene related criteria. Test results including positively selected sites can be visualized on the tree, and on the protein sequence alignment.
STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.
This database provides a list of known carbohydrate sequences to which pathogenic organisms specifically adhere. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.
keywords: bacteria, disease, fungi, glycan, glycomics, glycosylation, oligosaccharide, pathogen, post-translational modification, sugar epitope, virus
The SWISS-2DPAGE database assembles data on proteins identified on various 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data and bibliographical references. In addition several 2-D PAGE and SDS-PAGE images are provided, showing the experimentally determined location of the protein, as well as a theoretical region where the protein might be found in the gel.
keywords: 2-D PAGE, animal, bacteria, database searching, disease, experimentally verified, fungi, gel electrophoresis, human, identification, knowledge resource, Make2ddb, mass spectrometry, MW, peptide mass fingerprinting, pI, post-translational modification, protein database, protein identification, proteome database, Swiss-Prot, vertebrate, visualization
SWISS-MODEL Repository is a database of protein structure homology models generated by the fully automated SWISS-MODEL modeling pipeline.