ExOrthist: a tool to infer exon orthologies at any evolutionary distance
Mostra el registre complet Registre parcial de l'ítem
- dc.contributor.author Márquez, Yamile
- dc.contributor.author Mantica, Federica
- dc.contributor.author Cozzuto, Luca
- dc.contributor.author Burguera, Demián
- dc.contributor.author Hermoso Pulido, Antonio
- dc.contributor.author Ponomarenko, Julia
- dc.contributor.author Roy, Scott W.
- dc.contributor.author Irimia Martínez, Manuel
- dc.date.accessioned 2021-12-13T10:48:12Z
- dc.date.available 2021-12-13T10:48:12Z
- dc.date.issued 2021
- dc.description.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).
- dc.description.sponsorship The research has been funded by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (ERC-StG-LS2-637591 to MI), the Spanish Ministerio de Ciencia (BFU2017-89201-P to MI, including and FPI PhD fellowship to FM), the “Centro de Excelencia Severo Ochoa 2013-2017” (SEV-2012-0208), EMBO Long Term postdoctoral fellowship (ALTF 1505-2015 to YM), and Marie Skłodowska-Curie actions (MSCA) grant (705938 to YM). We acknowledge the support of the CERCA Programme/Generalitat de Catalunya and of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership
- dc.format.mimetype application/pdf
- dc.identifier.citation 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
- dc.identifier.doi http://dx.doi.org/10.1186/s13059-021-02441-9
- dc.identifier.issn 1474-760X
- dc.identifier.uri http://hdl.handle.net/10230/49181
- dc.language.iso eng
- dc.publisher BioMed Central
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/637591
- dc.relation.projectID info:eu-repo/grantAgreement/EC/H2020/705938
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PE/BFU2017-89201-P
- dc.rights © Yamile Márquez et al. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri https://creativecommons.org/licenses/by/4.0/
- dc.subject.other Genètica
- dc.subject.other Genòmica
- dc.subject.other Exons
- dc.subject.other Empalmament (Genètica)
- dc.title ExOrthist: a tool to infer exon orthologies at any evolutionary distance
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion