{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,5]],"date-time":"2025-12-05T15:31:26Z","timestamp":1764948686723,"version":"3.46.0"},"reference-count":28,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,11,22]],"date-time":"2025-11-22T00:00:00Z","timestamp":1763769600000},"content-version":"vor","delay-in-days":331,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Funda\u00e7\u00e3o para a Ci\u00eancia e Tecnologia","award":["2020.08608.BD"],"award-info":[{"award-number":["2020.08608.BD"]}]},{"DOI":"10.13039\/100008398","name":"VILLUM FONDEN","doi-asserted-by":"publisher","award":["42153"],"award-info":[{"award-number":["42153"]}],"id":[{"id":"10.13039\/100008398","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Center for Global Mountain Biodiversity","award":["25925"],"award-info":[{"award-number":["25925"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,12,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>High-fidelity genome assemblies provide unprecedented opportunities to decipher mechanisms of molecular evolution and phenotype landscapes. Here, we present PseudoChecker2, a command-line version of the web-tool PseudoChecker with expanded functions. It identifies gene loss via drastic mutational events such as premature stop codons, deletions and insertions. It enables the investigation of cross-species genomic datasets through: (i) integration into automated workflows, (ii) multiprocessing capability, and (iii) creation of a functional reference from annotation files. In addition, we introduce PseudoViz, a novel graphical interface designed to help interpret the results of PseudoChecker2 with intuitive visualizations. These tools combine the versatility and automation of a command-line tool with the user-friendliness of a graphical interface to tackle the challenges of the Genome Era.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>PseudoChecker2 and PseudoViz are fully available at https:\/\/github.com\/rresendepinto\/PseudoChecker2and \u00a0https:\/\/github.com\/rresendepinto\/PseudoViz.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioadv\/vbaf202","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T13:31:15Z","timestamp":1763731875000},"source":"Crossref","is-referenced-by-count":0,"title":["PseudoChecker2 and PseudoViz: automation and visualization of gene loss in the Genome Era"],"prefix":"10.1093","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4743-0457","authenticated-orcid":false,"given":"Rui","family":"Resende-Pinto","sequence":"first","affiliation":[{"name":"CIMAR\/CIIMAR \u2013 Interdisciplinary Centre of Marine and Environmental Research, University of Porto , 4450-208 Matosinhos,","place":["Portugal"]},{"name":"FCUP \u2013 Department of Biology, Faculty of Sciences, University of Porto (U. Porto) , 4169-007 Porto,","place":["Portugal"]}]},{"given":"Raquel","family":"Ruivo","sequence":"additional","affiliation":[{"name":"CIMAR\/CIIMAR \u2013 Interdisciplinary Centre of Marine and Environmental Research, University of Porto , 4450-208 Matosinhos,","place":["Portugal"]}]},{"given":"Josefin","family":"Stiller","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Copenhagen , 2100 Copenhagen,","place":["Denmark"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2805-4698","authenticated-orcid":false,"given":"Rute","family":"Fonseca","sequence":"additional","affiliation":[{"name":"Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen , 2100 Copenhagen,","place":["Denmark"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7697-386X","authenticated-orcid":false,"given":"Lu\u00eds Filipe C","family":"Castro","sequence":"additional","affiliation":[{"name":"CIMAR\/CIIMAR \u2013 Interdisciplinary Centre of Marine and Environmental Research, University of Porto , 4450-208 Matosinhos,","place":["Portugal"]},{"name":"FCUP \u2013 Department of Biology, Faculty of Sciences, University of Porto (U. Porto) , 4169-007 Porto,","place":["Portugal"]}]}],"member":"286","published-online":{"date-parts":[[2025,11,22]]},"reference":[{"key":"2025120510271483400_vbaf202-B1","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1038\/nrg.2016.39","article-title":"Evolution by gene loss","volume":"17","author":"Albalat","year":"2016","journal-title":"Nat Rev Genet"},{"key":"2025120510271483400_vbaf202-B2","doi-asserted-by":"crossref","first-page":"W321","DOI":"10.1093\/nar\/gkaa408","article-title":"PseudoChecker: an integrated online platform for gene inactivation inference","volume":"48","author":"Alves","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025120510271483400_vbaf202-B3","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1186\/1471-2164-9-466","article-title":"Retrocopy contributions to the evolution of the human genome","volume":"9","author":"Baertsch","year":"2008","journal-title":"BMC Genomics"},{"key":"2025120510271483400_vbaf202-B4","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1101\/gr.1860604","article-title":"An overview of ensembl","volume":"14","author":"Birney","year":"2004","journal-title":"Genome Res"},{"key":"2025120510271483400_vbaf202-B5","first-page":"20132669","article-title":"Recurrent gene loss correlates with the evolution of stomach phenotypes in gnathostome history","volume":"281","author":"Castro","year":"2014","journal-title":"Proc Biol Sci"},{"key":"2025120510271483400_vbaf202-B6","doi-asserted-by":"crossref","first-page":"143","DOI":"10.3390\/d11090143","article-title":"Total-evidence framework reveals complex morphological evolution in nightbirds (Strisores)","volume":"11","author":"Chen","year":"2019","journal-title":"Diversity"},{"key":"2025120510271483400_vbaf202-B7","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: freely available Python tools for computational molecular biology and bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"2025120510271483400_vbaf202-B8","unstructured":"Dainat J. \u00a0Agat: another Gff analysis toolkit to handle annotations in any GTF\/GFF format. 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