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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159060.pdf - Published Version Available under License Creative Commons Attribution. 6MB |
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 |
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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 > School of Infection & Immunity |
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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