genbank_to_gene

genbank_to_gene converts GenBank files into .ffn gene sequence files for downstream genomic analyses.

Key Features:

• GenBank to .ffn conversion: Parses GenBank files and extracts nucleotide gene sequences to generate .ffn files.
• Galaxy integration and HPC execution: Operates within the Galaxy platform and can execute on high-performance computing resources at Institut Pasteur.
• Automation and reproducibility: Conversion is automated within Galaxy to support reproducible and transparent computational analyses.
• API and Bioblend interoperability: Communicates with Galaxy via the Galaxy API or the Bioblend library to manage execution and data transfer.

Scientific Applications:

• Gene prediction and annotation: Provides .ffn nucleotide gene sequences as input for gene prediction and functional annotation workflows.
• Comparative genomics: Generates gene sequence datasets in .ffn format for comparative genomics analyses.
• Metagenomic analysis: Converts GenBank-formatted data into .ffn files for metagenomic analysis workflows.
• Phylogenetic studies: Supplies gene sequences in .ffn format for phylogenetic inference and tree reconstruction.

Methodology:

Parses GenBank files (nucleotide sequences with annotations) and extracts gene sequences to generate .ffn files, with the conversion process automated within the Galaxy platform.