FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes.

> 商业许可源文 · EUROPE_PMC · [CC-BY](https://creativecommons.org/licenses/by/)

书目信息

引用：Basenko EY, Pulman JA, Shanmugasundram A, Harb OS, Crouch K, Starns D, Warrenfeltz S, Aurrecoechea C, Stoeckert CJ, Kissinger JC, Roos DS, Hertz-Fowler C. (2018). FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. Journal of fungi (Basel, Switzerland). PMID 30152809 · PMC5872342 · DOI 10.3390/jof4010039

证据类型：DATABASE_RESOURCE

主题：rna-seq、proteomics

被引次数（采集时）：290

原始记录：[Europe PMC](https://europepmc.org/article/MED/30152809)

来源许可：[CC-BY](https://creativecommons.org/licenses/by/)

作者摘要（按来源许可复用）

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.

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