FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Basenko, Evelina Y ORCID: 0000-0001-8611-5447, Pulman, Jane A, Shanmugasundram, Achchuthan ORCID: 0000-0003-2349-6929, Harb, Omar S, Crouch, Kathryn, Starns, David ORCID: 0000-0001-6583-9067, Warrenfeltz, Susanne, Aurrecoechea, Cristina, Stoeckert, Christian J Jr, Kissinger, Jessica C
et al (show 2 more authors) (2018) FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. JOURNAL OF FUNGI, 4 (1). E39-.

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FungiDB ( 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, 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, <i>Aspergillus</i> 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.

Item Type: Article
Uncontrolled Keywords: fungi, pathogen, bioinformatics, omics, genomics, transcriptomics, proteomics, sequence analysis, RNA-Seq, Galaxy
Depositing User: Symplectic Admin
Date Deposited: 24 Apr 2018 06:30
Last Modified: 07 Feb 2024 06:28
DOI: 10.3390/jof4010039
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