Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02441-9
Keywords
Alternative splicing; Orthology; Paralogy; Intron-exon structures
Funding
- European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program [ERC-StG-LS2-637591]
- Spanish Ministerio de Ciencia [BFU2017-89201-P]
- Centro de Excelencia Severo Ochoa 2013-2017 [SEV-2012-0208]
- EMBO Long Term postdoctoral fellowship [ALTF 1505-2015]
- Marie Sklodowska-Curie actions (MSCA) grant [705938]
- CERCA Programme/Generalitat de Catalunya
- Spanish Ministry of Economy, Industry and Competitiveness (MEIC)
- Marie Curie Actions (MSCA) [705938] Funding Source: Marie Curie Actions (MSCA)
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ExOrthist is a Nextflow-based software that enables inference of exon homologs and orthogroups, visualization of evolution of exon-intron structures, and assessment of conservation of alternative splicing patterns. It evaluates exon sequence conservation by considering the surrounding exon-intron context to derive genome-wide multi-species exon homologies.
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).
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