{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:53:14Z","timestamp":1761897194020},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2020,1,3]],"date-time":"2020-01-03T00:00:00Z","timestamp":1578009600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"BCCM\/LMG Bacteria Collection and Belgian Nuclear Research Centre"},{"name":"Federal Public Planning Service\u2014Science Policy, Belgium"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>One of the most widespread methods used in taxonomy studies to distinguish between strains or taxa is the calculation of average nucleotide identity. It requires a computationally expensive alignment step and is therefore not suitable for large-scale comparisons. Short oligonucleotide-based methods do offer a faster alternative but at the expense of accuracy. Here, we aim to address this shortcoming by providing a software that implements a novel method based on short-oligonucleotide frequencies to compute inter-genomic distances.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Our tetranucleotide and hexanucleotide implementations, which were optimized based on a taxonomically well-defined set of over 200 newly sequenced bacterial genomes, are as accurate as the short oligonucleotide-based method TETRA and average nucleotide identity, for identifying bacterial species and strains, respectively. Moreover, the lightweight nature of this method makes it applicable for large-scale analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The method introduced here was implemented, together with other existing methods, in a dependency-free software written in C, GenDisCal, available as source code from https:\/\/github.com\/LM-UGent\/GenDisCal. The software supports multithreading and has been tested on Windows and Linux (CentOS). In addition, a Java-based graphical user interface that acts as a wrapper for the software is also available.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz964","type":"journal-article","created":{"date-parts":[[2019,12,30]],"date-time":"2019-12-30T20:11:11Z","timestamp":1577736671000},"page":"2337-2344","source":"Crossref","is-referenced-by-count":10,"title":["PaSiT: a novel approach based on short-oligonucleotide frequencies for efficient bacterial identification and typing"],"prefix":"10.1093","volume":"36","author":[{"given":"Gleb","family":"Goussarov","sequence":"first","affiliation":[{"name":"Microbiology Unit, Belgian Nuclear Research Centre (SCK\u2022CEN) , Mol, Belgium"},{"name":"Laboratory of Microbiology and BCCM\/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University , Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ilse","family":"Cleenwerck","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and BCCM\/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University , Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mohamed","family":"Mysara","sequence":"additional","affiliation":[{"name":"Microbiology Unit, Belgian Nuclear Research Centre (SCK\u2022CEN) , Mol, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Natalie","family":"Leys","sequence":"additional","affiliation":[{"name":"Microbiology Unit, Belgian Nuclear Research Centre (SCK\u2022CEN) , Mol, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pieter","family":"Monsieurs","sequence":"additional","affiliation":[{"name":"Microbiology Unit, Belgian Nuclear Research Centre (SCK\u2022CEN) , Mol, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guillaume","family":"Tahon","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and BCCM\/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University , Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aur\u00e9lien","family":"Carlier","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and BCCM\/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University , Ghent, Belgium"},{"name":"LIPM, Universit\u00e9 de Toulouse, INRAE , CNRS, Castanet-Tolosan, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peter","family":"Vandamme","sequence":"additional","affiliation":[{"name":"Laboratory of Microbiology and BCCM\/LMG Bacteria Collection, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University , Ghent, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rob","family":"Van Houdt","sequence":"additional","affiliation":[{"name":"Microbiology Unit, Belgian Nuclear Research Centre (SCK\u2022CEN) , Mol, Belgium"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2020,1,3]]},"reference":[{"key":"2023013110172216100_btz964-B1","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1007\/3-540-44503-X_27","volume-title":"Database Theory\u2014ICDT 2001","author":"Aggarwal","year":"2001"},{"key":"2023013110172216100_btz964-B2","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1139\/gen-2015-0175","article-title":"bcgTree: automatized phylogenetic tree building from bacterial core genomes","volume":"59","author":"Ankenbrand","year":"2016","journal-title":"Genome"},{"key":"2023013110172216100_btz964-B3","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"2023013110172216100_btz964-B4","doi-asserted-by":"crossref","first-page":"4665","DOI":"10.1128\/JCM.43.9.4665-4673.2005","article-title":"Multilocus sequence typing scheme that provides both species and strain differentiation for the Burkholderia cepacia complex","volume":"43","author":"Baldwin","year":"2005","journal-title":"J. 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