bioRxivBioinformaticsPreprint
Protocol for GDT, Gene Dictionary Tool, to create and implement a gene dictionary across annotated genomes
B. DupiniD, Matheus Sanitá LimaiD, Alexandre Rossi PaschoaliD, David Roy SmithiD
Abstract
The Gene Dictionary Tool is a protocol for the creation and implementation of gene dictionaries across annotated genomes. Through a Python CLI (Command Line Interface), 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). We showcase GDTs functionalities by creating a gene dictionary for fungal mitochondrial genomes.
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