Tigre: uma ferramenta escalável para extração de regiões intergênicas a partir de anotações GFF3

Abstract

The extraction of intergenic regions from genomic annotation files is essential for comparative genomics and evolutionary biology studies, but presents computational challenges when dealing with overlapping features, circular genomes, and large-scale processing. The overall objective of this work is to present TIGRE (Tool for Intergenic Regions Extraction), a command-line tool developed in Python for automated extraction of intergenic regions from GFF3 files. Originally conceived as a preprocessing step in a research project on plant organelles, the tool was generalized and transformed into a standalone solution, currently undergoing publication in STAR Protocols journal. TIGRE implements a pipeline of three sequential commands: clean, for preparation and standardization of GFF3 files, including overlap resolution and fragmentation of features spanning circular genome boundaries; extract, for identification and annotation of inter- genic regions; and getfasta, for retrieval of nucleotide sequences. The architecture supports both single-genome and batch processing, with parallelization via multiprocessing and memory optimization through server-client architecture when integrated with the GDT tool. Validation was performed through processing of 1,207 plant mitochondrial genomes, demonstrating efficient execution with total time of 11.1 seconds on server and maximum memory consumption of 155.7 MB. The tool is available as open-source software under MIT license, distributed via PyPI, and has already processed over 35,000 genomes in its continued use in the original research project. TIGRE represents a significant contribution to the bioinformatics community, offering a robust, scalable, and flexible solution for intergenic region extraction, facilitating large-scale comparative genomic analyses.