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IPD-IMGT/HLA / Immune Polymorphism Database-IMGT/HLA
A locus-specific database for the hyper-polymorphic allele sequences of the genes in the human major histocompatibility (HLA) system. The IPD-IMGT/HLA database was developed to provide a centralized system for the study of polymorphism in genes of the immune system. The database is the official repository for the World Health Organization (WHO) Nomenclature Committee for Factors of the HLA System, and is the only way of receiving an official allele designation for a sequence.
Interferome
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Contains type I, II and III interferon (IFN) regulated genes. Interferome is a database that enables the reliable identification of interferon regulated gene (IRG) signatures from high-throughput data sets. It can assist in identifying regulatory elements and enable comparison of normal tissue expression of IRGs in human and mouse. The database allows users to search across data sets to explore biological drivers of IFN responses.
IMGT / international ImMunoGeneTics information system
A high-quality integrated knowledge resource specialized in the immunoglobulins or antibodies, T cell receptors, major histocompatibility complex, of human and other vertebrate species, and related proteins of the immune systems of any species. IMGT comprises 7 databases, 17 online tools and 15 000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data.
IEDB-AR
Provides access to well-documented and tested epitope-related tools through a common style of web interface. IEDB-AR is a database that allows users to easily make direct comparisons between and among various prediction methods. The IEDB-AR provides five analytical tools for: (i) calculating the epitope population coverage; (ii) assessing the degree of conservancy of an epitope; (iii) visualization and analysis of 3D structures of molecules containing epitopes; (iv) clustering of epitope sequences and (v) mapping of epitopes onto 3D protein structures.
IPD / Immuno Polymorphism Database
A set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory.
IPD-MHC / Immuno Polymorphism Database-Major Histocompatibility Complex
A repository to collect and expertly curate sequences of the major histocompatibility complex from non-human species. The IPD-MHC Database has been designed to accommodate the large amounts of data on sequence variants and be easily expandable. Curators can edit and update each MHC group’s section, and new taxonomic groups can be simply assigned. This database introduces a new data organization and submission pipeline, providing a scalable and manageable system, while maintaining the high level of curation.
EPIMHC
A relational database of MHC-binding peptides and T cell epitopes that are observed in real proteins. Currently, the database contains 4867 distinct peptide sequences from various sources, including 84 tumor-associated antigens. The EPIMHC database is accessible through a web server that has been designed to facilitate research in computational vaccinology. Importantly, peptides resulting from a query can be selected to derive specific motif-matrices. Subsequently, these motif-matrices can be used in combination with a dynamic algorithm for predicting MHC-binding peptides from user-provided protein queries.
McPAS-TCR
Provides T cell receptor (TCR) sequences associated with various pathologies and antigens. McPAS-TCR aims to assemble information on pathology-related TCR sequences by extracting information from published literature. It offers more than 5 100 sequences of TCRs related with various pathologic conditions and the antigens associated with everyone. The database is manually curated and is consultable by T cell type, tissue, epitope, source organism, major histocompatibility complex (MHC) restriction, assay type and other criteria.
Epipox
Provides data about predicted T-cell epitome. Epipox is organised around three different axes: peptides, predictions, and proteins. It contains about 18700 human leukocyte antigen (HLA) I and 32700 HLA II-restricted peptides, each identified by its sequence and restriction element. This tool provides annotations on whether the proteins have transmembrane region or leader signal sequence, as proteins with these features often interact with host cells and are important targets for subunit vaccine design.
HLAsupE / Human Leucocyte Antigens supertype-specific Epitopes
Provides an integrated database of human leukocyte antigens (HLAs) supertype-specific epitopes. HLAsupE is an online resource of promiscuous T cell epitopes that is organized based on the HLA supertypes. Each of the supertype-specific peptides in this resource was annotated in terms of its cross-reactivity to HLA molecules within the same supertype. It can be used as a resource for the development of epitope-based vaccines and immunotherapies with broad coverage of human population.
TANTIGEN
Provides a data resource for analysis of tumor antigens and their functional sites. TANTIGEN is a comprehensive database of tumor T cell antigens that provides a catalog of previously published works and a repository of validated epitopes for cross-referencing newly discovered peptides. A training set for prediction of Human Leucocyte Antigen (HLA) binders that are naturally processed, and construction of models for prediction of T cell response to HLA binders are also available. The database includes a selection of bioinformatics tools for data analysis.
HLA-ADR / The HLA and Adverse Drug Reaction Database
An open database listing known adverse drug reactions with Human leukocyte antigens (HLA) alleles. The HLA-ADR has been implemented within the wider Allele Frequency Net Database (AFND), which stores large collections of data on the allele and haplotype frequencies for healthy, worldwide populations, as well as modules for exploring immunogenetic disease associations. HLA-ADR provides a resource that not only facilitates meta-analyses but also enables users to further their investigations by using resources available with the main AFND website, e.g. on the incidence of particular HLA alleles/haplotypes in healthy worldwide populations.
ESTDAB / the European Searchable Tumour line DAtaBase
Compiles information about tumour cell lines. ESTDAB provides a resource which collects mainly melanoma and provides information about multiple features such as human leukocyte antigen (HLA) genotype and surface expression of HLA molecules, antigen processing capability, or apoptosis regulation. The database also includes a dictionary for supplying a detailed list of all recorded markers. Queries can be made by both simple search and multi-parameter search.
ProPepper
A database of cereal prolamin epitopes, peptides and proteins for expert users that are dealing with protein chemistry, proteomics and mass spectrometry, method developments and related applications in food science, agricultural breeding or medical studies. ProPepper™ contains the full scale of currently available prolamin sequences and specific in silico digested peptide entries, links to reference databases (Uniprot, NCBI & IEDB) and cross-referenced connections. The interface allows advanced global and parametric search functions along with a download option, with direct connections to the relevant public databases.
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