interelementgff

interelementgff generates GFF (General Feature Format) annotations for genomic regions located between pairs of consecutive annotated elements to enable analysis of inter-element sequences.

Key Features:

• GFF Output Generation: Produces GFF (General Feature Format) files that annotate regions between consecutive genomic elements.
• Inter-element Detection: Identifies consecutive annotated elements in a genome and defines the intervening regions.
• Galaxy Integration: Operates within the Galaxy framework to leverage its computational infrastructure.
• API-based Execution: Supports execution via the Galaxy API and the Bioblend library.
• Cluster Workflows: Executes automated workflows on the Institut Pasteur computational cluster.

Scientific Applications:

• Genomic Research: Enables analysis of inter-element and non-coding regions relevant to gene regulation and genome function.
• Metagenomics Analysis: Provides inter-element annotations useful in metagenomic workflows such as MetaGenSense.
• Phylogenetic Studies: Supplies detailed genomic region annotations that can be integrated with tools like NGphylogeny.fr for evolutionary analyses.

Methodology:

Operates within the Galaxy framework, identifies consecutive elements in input genomic annotations, generates GFF outputs for the intervening regions, and executes these steps via automated workflows using the Galaxy API/Bioblend on the Institut Pasteur cluster.