FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes

Journal of Fungi
Evelina Y BasenkoChristiane Hertz-Fowler

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 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.

References

Dec 19, 2003·Nucleic Acids Research·Rolf ApweilerLai-Su L Yeh
Dec 31, 2005·Nucleic Acids Research·Rainer WinnenburgKim E Hammond-Kosack
Mar 18, 2009·Bioinformatics·Cole TrapnellSteven L Salzberg
May 22, 2010·BMC Genomics·Dale GodfreyHans Thordal-Christensen
Oct 16, 2010·Methods in Enzymology·Christina A Cuomo, Bruce W Birren
Oct 29, 2010·Genome Biology·Simon Anders, Wolfgang Huber
Dec 1, 2010·Nucleic Acids Research·Donna MaglottTatiana Tatusova
Jul 27, 2011·PloS One·Fran SupekTomislav Šmuc
Nov 9, 2011·Nucleic Acids Research·Jason E StajichDavid S Roos
Nov 24, 2011·Nucleic Acids Research·J Michael CherryEdith D Wong
Dec 21, 2012·Science Translational Medicine·Gordon D BrownTheodore C White
Nov 15, 2013·Nucleic Acids Research·Henrik NordbergInna Dubchak
Nov 28, 2013·Nucleic Acids Research·Jaime Huerta-CepasToni Gabaldón
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
May 9, 2014·PLoS Neglected Tropical Diseases·Patrícia de Sousa LimaCélia Maria de Almeida Soares
Sep 28, 2014·Bioinformatics·Simon AndersWolfgang Huber
Oct 2, 2014·Molecular Plant-microbe Interactions : MPMI·Carmen Ruiz-RoldánM Isabel G Roncero
Oct 25, 2014·Concurrency and Computation : Practice & Experience·Ravi K MadduriIan T Foster
Nov 2, 2014·Nucleic Acids Research·Mark D McDowallValerie Wood
Oct 18, 2015·Nucleic Acids Research·Minoru KanehisaMao Tanabe
Nov 22, 2015·Nucleic Acids Research·Karen ClarkEric W Sayers
Dec 22, 2015·Nucleic Acids Research·Andrew YatesPaul Flicek
Sep 21, 2016·Emerging Infectious Diseases·Jason A NobleJohn N Galgiani
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The Gene Ontology Consortium
Dec 3, 2016·Nucleic Acids Research·Cristina AurrecoecheaJie Zheng
Jul 1, 2017·PLoS Neglected Tropical Diseases·Síle F MolloyAngela Loyse
Jan 23, 2018·Fungal Genetics and Biology : FG & B·Thomas T BaldwinPhil P Bregitzer

❮ Previous
Next ❯

Citations

Nov 6, 2018·Metallomics : Integrated Biometal Science·Matthias MisslingerHubertus Haas
Jan 30, 2019·Applied Microbiology and Biotechnology·Kevin SchmitzJ Philipp Benz
May 30, 2019·Microbiology·Maria MaryamCarolina Coelho
Jul 25, 2019·EMBO Reports·Silke JankowskiMichael Feldbrügge
Nov 17, 2019·Nucleic Acids Research·Martin UrbanKim E Hammond-Kosack
Feb 8, 2020·Rapid Communications in Mass Spectrometry : RCM·Zhilong LinPiliang Hao
Sep 25, 2019·Nature Microbiology·Caitlin H KowalskiRobert A Cramer
May 7, 2020·Pathogens·Sephra N Rampersad
Jun 3, 2020·Molecular Plant-microbe Interactions : MPMI·Sean P O'MaraH Corby Kistler
Apr 9, 2020·BMC Biology·Caitlin LoefflerSerghei Mangul
Jan 31, 2019·Non-coding RNA·Hua XiaoPatrick K T Shiu
Mar 3, 2020·Frontiers in Microbiology·Ingo BauerStefan Graessle
Aug 28, 2020·Proceedings of the National Academy of Sciences of the United States of America·Caitlin H KowalskiRobert A Cramer
Jul 22, 2020·Molecular Microbiology·Kristina ShostakRajagopal Subramaniam
Mar 21, 2018·Journal of Fungi·Theo N Kirkland
Jun 16, 2019·International Journal of Molecular Sciences·Olufunmilayo Olukemi AkapoKhajamohiddin Syed
Jun 13, 2020·Frontiers in Cell and Developmental Biology·Su-Ting JiangTong-Bao Liu
Aug 9, 2020·Frontiers in Plant Science·Mohammad PourkheirandishMohan B Singh
Apr 14, 2020·Fungal biology and biotechnology·Vera MeyerHan A B Wösten
Oct 14, 2020·Environmental Microbiology·Ashley V NyweningJarrod R Fortwendel
Oct 16, 2020·Nature Communications·Mengyao NiuNancy P Keller
Jan 10, 2021·Journal of Fungi·François DanionJean-Paul Latgé

❮ Previous
Next ❯

Datasets Mentioned

BETA
ERR1360179
ERR1360193

Methods Mentioned

BETA
RNA-Seq
RNA Seq

Software Mentioned

BLASTP
EnsemblFungi
Globus Genomics
Galaxy
GO Summaries R package
HTseq
Metabolic Pathway Enrichment
Ensembl
Gene Ontology
Genomic Colocation

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.