Table 1.

Currently active filamentous fungi databases, genome browsers, and training.

Database and Website	Usage	Reference
PHI-base - Pathogen-Host Interaction database http://www.phi-base.org/	PHI-base is a web-accessible database that catalogues experimentally verified pathogenicity, virulence, and effector genes from fungal, oomycete, and bacterial pathogens. PHI-base is invaluable to the discovery of genes of pathogens, which may be potential targets for chemical and/or other intervention. In collaboration with the FRAC (Fungicide Resistance Action Committee) team, PHI-base also includes antifungal compounds and their target genes.	[57,58]
DFVF—Database of virulence factors in fungal pathogens http://sysbio.unl.edu/DFVF/	Experimental biologists and computational biologists can use the database and/or the predicted virulence factors to guide their search for new virulence factors and/or discovery of new pathogen–host interaction mechanisms in fungi.	[59]
EnsemblFungi https://fungi.ensembl.org/index.html	Ensembl Fungi is a browser for fungal genomes. A majority of these are taken from the databases of the International Nucleotide Sequence Database Collaboration. Data can be visualised through the Ensembl genome browser.	[60]
FungiDB: Fungi Database https://fungidb.org/fungidb/	FungiDB belongs to the EuPathDB family of databases and integrates whole-genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.	[61,62]
JGI—MycoCosm https://mycocosm.jgi.doe.gov/mycocosm/home	MycoCosm enables users to navigate across sequenced fungal genomes and to conduct comparative and genome-centric analyses of fungi and community annotation “The 1000 fungal genomes project”.	[63,64]
JGI—GOLD—Genomes Online Database https://gold.jgi.doe.gov/	A manually curated data-management system that catalogues sequencing projects with associated metadata from around the world. GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) minimum information standards.	[65]
CFGP—Comparative Fungal Genomics Platform http://cfgp.riceblast.snu.ac.kr/main.php	The CFGP 2.0 (Comparative Fungal Genomics Platform): The CFGP interactive informatics workbench has an archive of 283 genomes corresponding to 152 fungal and oomycete species; 27 bioinformatics tools are available for users.	[66]
Fungal Pathogen Genomics https://coursesandconferences.wellcomegenomecampus.org/our-events/fungal-pathogen-genomics	Hands-on training in web-based, data-mining resources for fungal genomes. Comparative genomics, gene trees, whole-genome alignment; identification of orthologs and orthology-based inference; genome browsers and gene pages; RNA-Seq analysis and visualization in VEuPathDB Galaxy; variant calling analysis; development of advanced biologically relevant queries using FungiDB; and introduction to annotation and curation of fungal genomes.	Wellcome Genome Campus, Cambridge, UK