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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
Published on: August 15, 2019
Protocol for creating a gene dictionary for organelle genomes using the Gene Dictionary Tool
Breno Dupin1, Matheus Sanita Lima2, Alexandre Rossi Paschoal3
1Department of Computer Science, Federal University of Technology - Parana, Cornelio Procopio, PR 86300-000, Brazil.
Abstract:
Here, we present a protocol for creating a gene dictionary for fungal mitochondrial genomes using the Gene Dictionary Tool. Through a Python Command Line Interface (CLI), the user identifies what annotations are missing in the inputted dictionary. Via two Jupyter Notebooks, the user builds a gene dictionary based on attributes retrieved from inputted GFF3 files. The final output, a .gdict file, is findable, accessible, interoperable, and reusable (FAIR). This protocol can be adapted to create a gene dictionary for other genomes.
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