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J. Fungi 2018, 4(1), 39; https://doi.org/10.3390/jof4010039

FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

1
Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
2
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
3
Wellcome Trust Centre for Molecular Parasitology, Glasgow G12 8TA, UK
4
Center for Tropical and Emerging Global Diseases, Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
5
Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104, USA
These authors contributed equally to this work.
*
Authors to whom correspondence should be addressed.
Received: 31 January 2018 / Revised: 7 March 2018 / Accepted: 15 March 2018 / Published: 20 March 2018
(This article belongs to the Special Issue Genomic Data in Pathogenic Fungi)
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Abstract

FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that integrates genomic, transcriptomic, proteomic, and phenotypic datasets, and other types of data for pathogenic and nonpathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, Aspergillus Genome Database (AspGD), The Broad Institute, Joint Genome Institute (JGI), Ensembl, and other sources. FungiDB offers a user-friendly web interface with embedded bioinformatics tools that support custom in silico experiments that leverage FungiDB-integrated data. In addition, a Galaxy-based workspace enables users to generate custom pipelines for large-scale data analysis (e.g., RNA-Seq, variant calling, etc.). This review provides an introduction to the FungiDB resources and focuses on available features, tools, and queries and how they can be used to mine data across a diverse range of integrated FungiDB datasets and records. View Full-Text
Keywords: fungi; pathogen; bioinformatics; omics; genomics; transcriptomics; proteomics; sequence analysis; RNA-Seq; Galaxy fungi; pathogen; bioinformatics; omics; genomics; transcriptomics; proteomics; sequence analysis; RNA-Seq; Galaxy
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Basenko, E.Y.; Pulman, J.A.; Shanmugasundram, A.; Harb, O.S.; Crouch, K.; Starns, D.; Warrenfeltz, S.; Aurrecoechea, C.; Stoeckert, C.J., Jr.; Kissinger, J.C.; Roos, D.S.; Hertz-Fowler, C. FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. J. Fungi 2018, 4, 39.

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