Publication:20210824084044

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Publication
URL https://pubmed.ncbi.nlm.nih.gov/34416914/
Title ExOrthist: a tool to infer exon orthologies at any evolutionary distance

Authors Yamile Márquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy, Manuel Irimia
Date 2021-08-20

Publisher Genome Biology
DOI 10.1186/s13059-021-02441-9
Tag Alternative Splicing, Animals, Computational Biology, Conserved Sequence, Evolution, Molecular, Exons, Genome, Humans, Introns, Mice, Software, Alternative splicing, Intron-exon structures, Orthology, Paralogy



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 ).


Annotation We collaborated in making the tool reproducible and scalable using github-docker-nextflow.
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