What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species

FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integra...

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Vydáno v:Genetics (Austin) Ročník 227; číslo 1
Hlavní autoři: Basenko, Evelina Y, Shanmugasundram, Achchuthan, Böhme, Ulrike, Starns, David, Wilkinson, Paul A, Davison, Helen R, Crouch, Kathryn, Maslen, Gareth, Harb, Omar S, Amos, Beatrice, McDowell, Mary Ann, Kissinger, Jessica C, Roos, David S, Jones, Andrew
Médium: Journal Article
Jazyk:angličtina
Vydáno: United States 07.05.2024
Témata:
Computational Biology - methods
Databases, Genetic
Fungi - genetics
Genome, Fungal
Genomics - methods
Internet
Oomycetes - genetics
Software
Galaxy
database
omics
fungi
Apollo
data mining
oomycetes
bioinformatics
search strategy
web-based resource
ISSN:1943-2631, 1943-2631
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Shrnutí:FungiDB (https://fungidb.org) serves as a valuable online resource that seamlessly integrates genomic and related large-scale data for a wide range of fungal and oomycete species. As an integral part of the VEuPathDB Bioinformatics Resource Center (https://veupathdb.org), FungiDB continually integrates both published and unpublished data addressing various aspects of fungal biology. Established in early 2011, the database has evolved to support 674 datasets. The datasets include over 300 genomes spanning various taxa (e.g. Ascomycota, Basidiomycota, Blastocladiomycota, Chytridiomycota, Mucoromycota, as well as Albuginales, Peronosporales, Pythiales, and Saprolegniales). In addition to genomic assemblies and annotation, over 300 extra datasets encompassing diverse information, such as expression and variation data, are also available. The resource also provides an intuitive web-based interface, facilitating comprehensive approaches to data mining and visualization. Users can test their hypotheses and navigate through omics-scale datasets using a built-in search strategy system. Moreover, FungiDB offers capabilities for private data analysis via the integrated VEuPathDB Galaxy platform. FungiDB also permits genome improvements by capturing expert knowledge through the User Comments system and the Apollo genome annotation editor for structural and functional gene curation. FungiDB facilitates data exploration and analysis and contributes to advancing research efforts by capturing expert knowledge for fungal and oomycete species.
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ISSN:1943-2631
1943-2631
DOI:10.1093/genetics/iyae035