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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.

(last updated: Oct 12, 2019)

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Resource NameResource TypeDescriptionKeywordsResource IDProper CitationParent OrganizationRelated ConditionFunding AgencyRelationReferenceWebsite StatusAlternate IDsAlternate URLsOld URLs
FlyMineResource, data analysis service, data access protocol, production service resource, analysis service resource, database, web service, service resource, software resource, data or information resourceAn integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java APIanopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publicationSCR_002694(FlyMine, RRID:SCR_002694)University of Cambridge; Cambridge; United Kingdom NHGRI, Wellcome Trustrelated to: FlyBase, Universal Protein Resource, Ensembl, InterPro, BioGRID, Research Collaboratory for Structural Bioinformatics Protein Data Bank, Tree families database, IntAct, Gene Ontology, GOA, ArrayExpress, REDfly Regulatory Element Database for Drosophilia, KEGG, ReactomePMID:17615057Last checked upnif-0000-02845
FunTreeResource, data or information resource, databaseFunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms.enzyme function, enzyme superfamily, enzyme, sequence, structure, phylogenetic, chemical, mechanistic, functional annotation, superfamily, gold standardSCR_006014(FunTree, RRID:SCR_006014)European Bioinformatics Institute BBSRC, DOE, European Molecular Biology Laboratory; Heidelberg; Germany, Wellcome Trustrelated to: CATH: Protein Structure Classification, Research Collaboratory for Structural Bioinformatics Protein Data Bank, KEGG, UniProtKBPMID:22006843Last checked upnlx_151402
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