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KinMutBase is a comprehensive database of disease-causing mutations in protein kinase domains. The current release of the database contains 582 mutations in 20 tyrosine kinase domains and 13 serine/threonine kinase domains. The database refers 1790 cases from 1322 families. KinMutBase is a registry of mutations in human protein kinases related to disorders. Kinases are essential cellular signaling molecules, in which mutations can lead to diseases, including immunodeficiencies, cancers and endocrine disorders. Mutations appear both in conserved hallmark residues of the kinases as well as in non-homologous sites. The KinMutBase WWW pages provide plenty of information, namely mutation statistics and display, clickable sequences with mutations and changes to restriction enzyme patterns.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. Islander is a comprehensive online database containing genomic islands discovered in completely sequenced bacterial genomes by the algorithm. Islands are transmitted between prokaryotic strains and therefore play a major role in genome evolution. An island often encodes an integrase gene that specifies the island''s position in the host genome. Usually integrases specify tRNA genes, and the island splits the the tRNA gene when it integrates. However the island also carries sequence that replaces the split-off portion, restoring an intact tRNA gene. Thus an island is often marked by a tRNA gene at one end, and a fragment of that gene at the other end. The islands in this database were identified using this principle through the following procedure: :1. Search for tRNA and tmRNA genes using tRNAscan-SE and BRUCE on whole prokaryotic genomes. :2. Search for significant hits to each tRNA and tmRNA gene using BLAST against the source genome. :3. Narrow down hits to those containing integrase genes (required for site-specific integration into the host genome). :4. Remove false positives (e.g., tRNA gene fragment not from end of gene, or in wrong orientation). :5. Enter into mysql database, display on website using Perl CGI pages., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 17 years ago - by Anonymous

A database and web application to annotate disease-related and functionally important amino acids in human proteins., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 13 years ago - by Anonymous

It catalogues the influenza sequence and epitope information obtained in Asia and currently hosts a total of 33388 influenza A and 4762 influenza B virus sequence data collected in 21 countries, and a total of 545 amantadine-resistant influenza virus sequences collected in Korea. ISED provides users with pre-built application tools to analyze sequence alignment and difference patterns and allows users to visualize epitope matching structures.

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• SciCrunch
• 17 years ago - by Anonymous

IRIS is the rice implementation of the International Crop Information System (ICIS) which is a database system that provides integrated management of global information on genetic resources and crop cultivars. This includes germplasm pedigrees, field evaluations, structural and functional genomic data (including links to external plant databases) and environmental (GIS) data.

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• SciCrunch
• 17 years ago - by Anonymous

Database of experimentally verified IRES structures. Presents information about experimentally studied Internal Ribosome Entry Site segments.

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• SciCrunch
• 17 years ago - by Anonymous

iProLINK (integrated Protein Literature, INformation and Knowledge) has been developed as a resource to facilitate text mining in the area of literature-based database curation, named entity recognition, and protein ontology development. The collection of data sources can be utilized by computational and biological researchers to explore literature information on proteins and their features or properties. The data sources for bibliography mapping and feature evidence attribution include mapped citations (PubMed ID to protein entry and feature line mapping) and annotation-tagged literature corpora. The latter includes several hundred abstracts and full-text articles tagged with experimentally validated post-translational modifications (PTMs) annotated in the PIR protein sequence database.

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• SciCrunch
• 17 years ago - by Anonymous

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• SciCrunch
• 15 years ago - submitted by Eddy Kim

L1Base is a dedicated database containing putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included in the database.

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• SciCrunch
• 17 years ago - by Anonymous

The IPD - MHC Database provides a centralized repository for sequences of the major histocompatibility complex from a number of different species. Through a number of international collaborations IPD is able to provide the MHC sequences of different species. The sequences provided by each group are curated by experts in the field and then submitted to the central database.

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• SciCrunch
• 17 years ago - by Anonymous

The IPD-KIR database provides a centralized repository for human KIR sequences. Killer-cell Immunoglobulin-like Receptors (KIR) have been shown to be highly polymorphic at the allelic and haplotypic level. KIRs are members of the immunoglobulin superfamily (IgSF) formerly called Killer-cell Inhibitory Receptors. They are composed of two or three Ig-domains, a transmembrane region and cytoplasmic tail which can in turn be short (activatory) or long (inhibitory). The Leukocyte Receptor Complex (LRC) which encodes KIR genes has been shown to be polymorphic, polygenic and complex like the MHC.

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• SciCrunch
• 17 years ago - by Anonymous

A centralised repository for the data which define the human platelet antigens (HPA). Alloantibodies against human platelet antigens are involved in neonatal alloimmune thrombocytopenia, post-transfusion purpura and refractoriness to random donor platelets. The Human Platelet Antigen (HPA) nomenclature system was adopted in 1990 to overcome problems with the previous nomenclature. Since then more antigens have been described and meanwhile the molecular basis of many has been resolved, and the nomenclature was revised in 2003.

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• SciCrunch
• 17 years ago - by Anonymous

The European Searchable Tumour Line Database (ESTDAB) Database and Cell Bank provide a service enabling investigators to search online for HLA typed, immunologically characterised tumour cells as part of the European Commission Fifth Framework Infrastructures Program. The following tools and pages are available in ESTDAB: :* Search ESTDAB on primary search determinants :* Search ESTDAB on all search determinants :* Dictionary of markers and techniques used

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. A collection of tools for exploring the molecular biology and genomics of C. elegans with a special emphasis on alternative splicing. It includes: Tracks Display- View splicing diagrams for any gene in the Sanger C. elegans database alongside cDNA and EST alignments. Retrieve DNA sequences with the exons in upper case. Search the literature. Alt Splicing Catalog - As defined by Chuck's altGraphX process. A frames based viewer linking to the genome browser. Alt-Splicing Catalog - A catalog of genes for which the cDNA and EST evidence indicates alternative splicing.

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• SciCrunch
• 17 years ago - by Anonymous

The Human Intermediate Filament Database is a continuously updated review of the intermediate filament field. It is hoped that users will contribute to the development and expansion of the database on a regular basis. Contributions may include novel variants, new patients with previously discovered sequence and allelic variants. Suggestions on ways to improve the database are also welcome. The entire database can be searched through the Browse and Search options. A number of different parameters can be used to search the database including unique identifier, intermediate filament, disease DNA variations, amino acid variations, domain, date accepted, author and abstract. Output from the search is returned in a table containing all the pertinent cross referenced information. Multiple sequence alignment can also be performed via the CLUSTALW program to determine cDNA or protein sequence conservation. The database is linked to multiple other resources including NCBI RefSeq, PDB, OMIM, UCSC genome browser, NCBI Gene, HomoloGene, PubMed and HGNC. In the case of HGNC, reciprocal links are also available from HGNC that links to Human Intermediate Filament Database. Due to the protein centric nature of the Human Intermediate Filament Database and the gene centric nature of HGNC, a HGNC record will potentially link to multiple records in this database due to the presence of alternative splicing. In such an event, the Human Intermediate Filament Database will present to the user a list of all the protein records resulting from the HGNC gene record. The database uses Jalview and Jmol applets for the visualization of multiple sequence alignment and structure respectively. The database contains information on disease phenotypes of a variety of different intermediate filament related diseases.

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• SciCrunch
• 17 years ago - by Anonymous

Interferome is a database that provides identification of interferon regulated gene signatures from high-throughput data sets (i.e. microarray, proteomic data etc.). It will also assist in identifying regulatory elements and enable comparison of tissue expression of IRGs in human and mouse. Availability of sequence information from more than 37 species, together with comprehensive annotation will enable comparative genomics and phylogenetic analysis to be performed on these IRGs. Within the database, Type I, II and III IFN regulated genes have been manually curated from more than 28 publicly available microarray datasets. Interferon Regulated Genes (IRGs) were identified from multiple microarray and proteomic experiments where cells were treated with IFNs. Genes that were up or down regulated more than 1.5 fold relative to control samples were defined as IRGs.

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• SciCrunch
• 17 years ago - by Anonymous

InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE). Interdom focuses on providing supporting evidence for validating and annotating detected protein interactions and complexes based on putative protein domain interactions. InterDom enhances the quality of in silico derivations by adopting an integrative strategy, assigning higher confidence to domain interactions that are independently derived from different data sources and methods.

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• SciCrunch
• 17 years ago - by Anonymous

This database identifies and characterizes all inter-chain beta-sheet interactions within entries in the Protein Data Bank (PDB) and within the corresponding hypothetical quaternary structures that are automatically generated at the European Bioinformatics Institute (EBI), and that are currently available through the Protein Quaternary Structure (PQS) server, within the Macromolecular Structure Database. The data are stored in a relational database. The database can be accessed through the Web and queried through a simple form. Entries can be ranked according to the relative structural importance of their inter-chain -sheet interactions, or according to other criteria. The ICBS database is intended as a tool to: :* further the study of -sheet protein-protein interactions :* identify new ICBS interactions as new structures are deposited and as old structures are revised in the Protein Data Bank :* help select targets for drug design.

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• SciCrunch
• 17 years ago - by Anonymous

The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.

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• SciCrunch
• 17 years ago - by Anonymous

Database of microsatellite characteristics of five fully sequenced insect genomes (fruit-fly, honeybee, malarial mosquito, red-flour beetle and silkworm). InSatDb allows users to obtain microsatellites annotated with size (in bp and repeat units); genomic location (exon, intron, up-stream or transposon); nature (perfect or imperfect); and sequence composition (repeat motif and GC%). One can access microsatellite cluster (compound repeats) information, and a list of microsatellites with conserved flanking sequences (microsatellite family or paralogs). InSatDb is complete with insect information, web links to find details, methodology and a tutorial. A separate Analysis section illustrates the comparative genomic analysis that can be carried out using the InSatDb output.

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• SciCrunch
• 17 years ago - by Anonymous