EuPathDB: the eukaryotic pathogen genomics database resource

Cristina Aurrecoechea, Ana Barreto, Evelina Y. Basenko, John Brestelli, Brian P. Brunk, Shon Cade, Kathryn Crouch, Ryan Doherty, Dave Falke, Steve Fischer, Bindu Gajria, Omar S. Harb (+18 others)
2016 Nucleic Acids Research  
The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are
more » ... with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polyso-mal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data.
doi:10.1093/nar/gkw1105 pmid:27903906 pmcid:PMC5210576 fatcat:gp4twmzt7rh2be7oga6xfszwpi