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

Márquez, Yamile; Mantica, Federica; Cozzuto, Luca; Burguera, Demián; Hermoso Pulido, Antonio; Ponomarenko, Julia; Roy, Scott W.; Irimia Martínez, Manuel

doi:http://dx.doi.org/10.1186/s13059-021-02441-9

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

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Márquez Y, Mantica F, Cozzuto L, Burguera D, Hermoso-Pulido A, Ponomarenko J et al. ExOrthist: a tool to infer exon orthologies at any evolutionary distance. Genome Biol. 2021 Aug 20;22(1):239. DOI: 10.1186/s13059-021-02441-9

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).