FungiDB: an integrated bioinformatic resource for fungi and oomycetes

Basenko, E. Y. et al. (2018) FungiDB: an integrated bioinformatic resource for fungi and oomycetes. Journal of Fungi, 4(1), 39. (doi:10.3390/jof4010039) (PMID:30152809) (PMCID:PMC5872342)

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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 non-pathogenic, free-living and parasitic organisms. FungiDB is one of the largest EuPathDB databases containing nearly 100 genomes obtained from GenBank, AspGD, The Broad 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:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Crouch, Dr Kathryn
Authors: Basenko, E. Y., Pulman, J. A., Shanmugasundram, A., Harb, O. S., Crouch, K., Starns, D., Warrenfeltz, S., Aurrecoechea, C., Stoeckert Jr., C. J., Kissinger, J. C., Roos, D. S., and Hertz-Fowler, C.
Subjects:Q Science > QH Natural history > QH301 Biology
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Journal of Fungi
Journal Abbr.:JoF
Publisher:MDPI
ISSN:2309-608X
ISSN (Online):2309-608X
Published Online:20 March 2018
Copyright Holders:Copyright © 2018 The Authors
First Published:First published in Journal of Fungi 4(1): 39
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
699381Cost-effective community access to integrated information for microbial eukaryotic pathogen researchMichael BarrettWellcome Trust (WELLCOTR)108443/Z/15/ZIII - PARASITOLOGY