{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T22:13:13Z","timestamp":1776204793803,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2024,4,1]],"date-time":"2024-04-01T00:00:00Z","timestamp":1711929600000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,3,29]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Sequence technology advancements have led to an exponential increase in bacterial genomes, necessitating robust taxonomic classification methods. The Percentage Of Conserved Proteins (POCP), proposed initially by Qin et al. (2014), is a valuable metric for assessing prokaryote genus boundaries. Here, I introduce a computational pipeline for automated POCP calculation, aiming to enhance reproducibility and ease of use in taxonomic studies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The POCP-nf pipeline uses DIAMOND for faster protein alignments, achieving similar sensitivity to BLASTP. The pipeline is implemented in Nextflow with Conda and Docker support and is freely available on GitHub under https:\/\/github.com\/hoelzer\/pocp. The open-source code can be easily adapted for various prokaryotic genome and protein datasets. Detailed documentation and usage instructions are provided in the repository.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae175","type":"journal-article","created":{"date-parts":[[2024,4,2]],"date-time":"2024-04-02T00:14:58Z","timestamp":1712016898000},"source":"Crossref","is-referenced-by-count":50,"title":["POCP-nf: an automatic Nextflow pipeline for calculating the percentage of conserved proteins in bacterial taxonomy"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7090-8717","authenticated-orcid":false,"given":"Martin","family":"H\u00f6lzer","sequence":"first","affiliation":[{"name":"Genome Competence Center (MF1), Robert Koch Institute , 13353 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2024,4,1]]},"reference":[{"key":"2024082904201069300_btae175-B1","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update","volume":"50","author":"Afgan","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2024082904201069300_btae175-B2","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.syapm.2016.09.004","article-title":"Phylogenomic re-assessment of the thermophilic genus Geobacillus","volume":"39","author":"Aliyu","year":"2016","journal-title":"Syst Appl Microbiol"},{"key":"2024082904201069300_btae175-B3","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2024082904201069300_btae175-B4","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1007\/s00203-022-03298-7","article-title":"Phylogenomic analysis of a metagenome-assembled genome indicates a new taxon of an anoxygenic phototroph bacterium in the family Chromatiaceae and the proposal of \u201cCandidatus thioaporhodococcus\u201d gen. nov","volume":"204","author":"Amulyasai","year":"2022","journal-title":"Arch Microbiol"},{"key":"2024082904201069300_btae175-B5","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.3390\/d14111009","article-title":"Anianabacter salinae gen. nov., sp. nov. 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