FungiDB: an integrated functional genomics database for fungi and oomycetes


David S. Roos 1 Evelina Basenko 2
1Department of Biology, FungiDB, University of Pennsylvania, Philadelphia, PA, USA
2Institute of Integrative Biology, University of Liverpool, Liverpool, UK

FungiDB (http://FungiDB.org) is a free online database that enables data mining and analysis of the pan-fungal and oomycetes genomic sequences and functional data. As part of the Eukaryotic Pathogen Bioinformatics Resource Center (http://EuPathDB.org), FungiDB enables users to conduct sophisticated searches and create in-silico experiments via an intuitive web-based graphical system. FungiDB contains genome sequence and annotation for over 75 species spanning the oomycetes and fungi, the latter including genomes of Agaricomycetes, Chytridiomycetes, Eurotiomycetes, Leotiomycetes, Pneumocystidomycetes, Pucciniomycetes, Saccharomycetes, Schizosaccharomycetes, Sordariomycetes, Tremellomycetes, Ustilaginomycetes, and Zygomycetes. In addition to genomic sequence data and annotation, users can explore functional data (eg. transcriptomics or proteomics), whole genome polymorphism data, metabolic pathways and results from genome wide analyses such as InterPro scan, signal peptide and transmembrane domain predictions, GO term and EC number associations and orthology profiles. FungiDB supports the capture of community knowledge in the form of user comments. Such comments may include free text updates and information, images, files, PubMed records, etc., and once submitted to FungiDB records (ie. gene pages) they become immediately visible and searchable. The graphical user interface in FungiDB allows users to conduct in silico experiments that leverage the available data and analyses. In addition, user datasets can be analyzed in the EuPathDB Galaxy instance, which offers preloaded genomes and several sample workflows for RNASeq and SNP analysis pipelines. Analysis results can be further explored and visualized in the FungiDB genome browser.

FungiDB is supported in part by NIH HHSN272201400030C and the Wellcome Trust grant WT108443MA