ExOrthist: a tool to infer exon orthologies at any evolutionary distance

Genome Biology

Yamile Márquez¹  Luca Cozzuto¹  Federica Mantica¹  Julia Ponomarenko¹  Demian Burguera¹  Antonio Hermoso-Pulido¹  Manuel Irimia¹  Scott W. Roy² 

[1] Centre for Genomic Regulation, Barcelona Institute of Science and Technology;San Francisco State University;

关键词: Alternative splicing;    Orthology;    Paralogy;    Intron-exon structures;   

DOI  :  10.1186/s13059-021-02441-9

来源: DOAJ

【 摘 要 】

Abstract Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ExOrthist, a fully reproducible Nextflow-based software enabling inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. ExOrthist evaluates exon sequence conservation and considers the surrounding exon-intron context to derive genome-wide multi-species exon homologies at any evolutionary distance. We demonstrate its use in different evolutionary scenarios: whole genome duplication in frogs and convergence of Nova-regulated splicing networks ( https://github.com/biocorecrg/ExOrthist ).

【 授权许可】

Unknown