{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T19:59:25Z","timestamp":1780516765746,"version":"3.54.1"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2022,2,2]],"date-time":"2022-02-02T00:00:00Z","timestamp":1643760000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Ministries of Economy and Competitiveness, and Science and Innovation","award":["BFU2016-77297-P"],"award-info":[{"award-number":["BFU2016-77297-P"]}]},{"name":"Ministries of Economy and Competitiveness, and Science and Innovation","award":["PID2020-114861GB-I00"],"award-info":[{"award-number":["PID2020-114861GB-I00"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,10]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Bacterial genomes are massively sequenced, and they provide valuable data to better know the complete set of genes of a species. The analysis of thousands of bacterial strains can identify both shared genes and those appearing only in the pathogenic ones. Current computational gene finders facilitate this task but often miss some existing genes. However, the present availability of different genomes from the same species is useful to estimate the selective pressure applied on genes of complete pangenomes. It may assist in evaluating gene predictions either by checking the certainty of a new gene or annotating it as a gene under positive selection. Here, we estimated the selective pressure of 19\u00a0271 genes that are part of the pangenome of the human opportunistic pathogen Acinetobacter baumannii and found that most genes in this bacterium are subject to negative selection. However, 23% of them showed values compatible with positive selection. These latter were mainly uncharacterized proteins or genes required to evade the host defence system including genes related to resistance and virulence whose changes may be favoured to acquire new functions. Finally, we evaluated the utility of measuring selection pressure in the detection of sequencing errors and the validation of gene prediction.<\/jats:p>","DOI":"10.1093\/bib\/bbac010","type":"journal-article","created":{"date-parts":[[2022,1,13]],"date-time":"2022-01-13T12:08:05Z","timestamp":1642075685000},"source":"Crossref","is-referenced-by-count":4,"title":["Assessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6736-6141","authenticated-orcid":false,"given":"Alejandro","family":"Rubio","sequence":"first","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA), Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, Sevilla 41013, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Juan","family":"Jimenez","sequence":"additional","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA), Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, Sevilla 41013, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3343-2822","authenticated-orcid":false,"given":"Antonio J","family":"P\u00e9rez-Pulido","sequence":"additional","affiliation":[{"name":"Centro Andaluz de Biologia del Desarrollo (CABD, UPO-CSIC-JA), Facultad de Ciencias Experimentales (\u00c1rea de Gen\u00e9tica), Universidad Pablo de Olavide, Sevilla 41013, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,2,2]]},"reference":[{"issue":"Suppl 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can contaminate public databases with spurious proteins containing spaced repeats","volume":"2020","author":"Rubio","year":"2020","journal-title":"Database (Oxford)"},{"key":"2022031506321828300_ref8","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1186\/1471-2105-11-119","article-title":"Prodigal: prokaryotic gene recognition and translation initiation site identification","volume":"11","author":"Hyatt","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"2022031506321828300_ref9","doi-asserted-by":"crossref","first-page":"6614","DOI":"10.1093\/nar\/gkw569","article-title":"NCBI prokaryotic genome annotation pipeline","volume":"44","author":"Tatusova","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2022031506321828300_ref10","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: rapid prokaryotic genome 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