Journal of integrative bioinformatics

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The official bioinformatics tool list for the Journal of Integrative Bioinformatics (JIB).

All bioinformatics tools published in JIB are automatically added to with first authors having the ability to edit their entries and directly import the tools information to

MycoDiversity DataBase (MDDB)

Database portal Web application 
Biodiversity Data integration and warehousing 
Fungi have crucial roles in ecosystems, and are important associates for many organisms. They are adapted to a wide variety of habitats, however their global distribution and diversity remains poorly documented. The exponential growth of DNA barcode information retrieved from the environment is assisting considerably the traditional ways for unraveling fungal diversity and detection. The raw DNA data in association to environmental descriptors of metabarcoding studies are made available in public sequence read archives. While this is potentially a valuable source of information for the investigation of Fungi across diverse environmental conditions, the annotation used to describe environment is heterogenous. Moreover, a uniform processing pipeline still needs to be applied to the available raw DNA data. Hence, a comprehensive framework to analyses these data in a large context is still lacking. We introduce the MycoDiversity DataBase, a database which includes public fungal metabarcoding data of environmental samples for the study of biodiversity patterns of Fungi. The framework we propose will contribute to our understanding of fungal biodiversity and aims to become a valuable source for large-scale analyses of patterns in space and time, in addition to assisting evolutionary and ecological research on Fungi.

JIB Publications
  • Martorelli I, Helwerda LS, Kerkvliet J, Gomes SIF, Nuytinck J, van der Werff CRA, Ramackers GJ, Gultyaev AP, Merckx VSFT, Verbeek FJ. Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).. J Integr Bioinform. 2020;. doi 10.1515/jib-2019-0046; PubMed 32463383