Publication:20210824084044
From Bioinformatics Core Wiki
| Publication | |
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| URL | https://pubmed.ncbi.nlm.nih.gov/34416914/ |
| Title | ExOrthist: a tool to infer exon orthologies at any evolutionary distance
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| Authors | Yamile Márquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy, Manuel Irimia |
| Date | 2021-08-20
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| 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 ).
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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