IGFinder

IGFinder: Intronless genes finder for an input species.

IGFinder is a script for identifying intronless genes for a particular organism. IGFinder works by using an ENSEMBL API.

Usage

python3 fetch_intronless_genes.py [optional species] (default gallus gallus) [/path/to/intron_UTR_db.txt]

Files

• fetch_intronless_genes.py:   Main script.
• fetch_genes.py:   Script containing helper functions for fetch_intronless_genes.py
• intron_UTR_db.txt:   Required intron database of genes with introns in the UTR region for several species (NOT uploaded to GitHub). The corresponding Intron file can be downloaded from https://drive.google.com/file/d/1c1t4eMQZ4SSHD0-iUiHph8eivTDYUq0l/view?usp=share_link.

Output

• {species}-multi_exon_genes.tsv:   Contains data of multi-exon genes.
• {species}-ui_single_exon_genes.tsv:   Contains data of UTR intron-containing single exon genes.
• {species}-intronless_genes.tsv:   Contains data of intronless genes.

Example

python3 fetch_intronless_genes.py "mus musculus" "/path/to/intron_UTR_db.txt"

Citation

Aviña-Padilla, K., Ramírez-Rafael, J. A., Herrera-Oropeza, G. E., Muley, V. Y., Valdivia, D. I., Díaz-Valenzuela, E., García-García, A., Varela-Echavarría, A., & Hernández-Rosales, M. (2021). Evolutionary Perspective and Expression Analysis of Intronless Genes Highlight the Conservation of Their Regulatory Role. Frontiers in genetics, 12, 654256. https://doi.org/10.3389/fgene.2021.654256