{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:56:02Z","timestamp":1773273362730,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2018,10,15]],"date-time":"2018-10-15T00:00:00Z","timestamp":1539561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","award":["281357"],"award-info":[{"award-number":["281357"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["179\/14"],"award-info":[{"award-number":["179\/14"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003977","name":"Israel Science Foundation","doi-asserted-by":"publisher","award":["939\/18"],"award-info":[{"award-number":["939\/18"]}],"id":[{"id":"10.13039\/501100003977","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Identification of conserved syntenic blocks across microbial genomes is important for several problems in comparative genomics such as gene annotation, study of genome organization and evolution and prediction of gene interactions. Current tools for syntenic block discovery do not scale up to the large quantity of prokaryotic genomes available today.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present a novel methodology for the discovery, ranking and taxonomic distribution analysis of colinear syntenic blocks (CSBs)\u2014groups of genes that are consistently located close to each other, in the same order, across a wide range of taxa. We present an efficient algorithm that identifies CSBs in large genomic datasets. The algorithm is implemented and incorporated in a novel tool with a graphical user interface, denoted CSBFinder, that ranks the discovered CSBs according to a probabilistic score and clusters them to families according to their gene content similarity. We apply CSBFinder to data mine 1487 prokaryotic genomes including chromosomes and plasmids. For post-processing analysis, we generate heatmaps for visualizing the distribution of CSB family members across various taxa. We exemplify the utility of CSBFinder in operon prediction, in deciphering unknown gene function and in taxonomic analysis of colinear syntenic blocks.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>CSBFinder software and code are publicly available at https:\/\/github.com\/dinasv\/CSBFinder.<\/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\/bty861","type":"journal-article","created":{"date-parts":[[2018,10,14]],"date-time":"2018-10-14T11:07:57Z","timestamp":1539515277000},"page":"1634-1643","source":"Crossref","is-referenced-by-count":11,"title":["CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes"],"prefix":"10.1093","volume":"35","author":[{"given":"Dina","family":"Svetlitsky","sequence":"first","affiliation":[{"name":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tal","family":"Dagan","sequence":"additional","affiliation":[{"name":"Institute of General Microbiology, Christian-Albrechts University Kiel, Kiel, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vered","family":"Chalifa-Caspi","sequence":"additional","affiliation":[{"name":"Bioinformatics Core Facility, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michal","family":"Ziv-Ukelson","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Ben-Gurion University of the Negev, Beer-Sheva, Israel"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,10,15]]},"reference":[{"key":"2023013107481531100_bty861-B1","doi-asserted-by":"crossref","first-page":"11436","DOI":"10.1016\/S0021-9258(19)38417-0","article-title":"Nucleotide sequence and genetic characterization reveal six essential genes for the liv-i and ls transport systems of escherichia coli","volume":"265","author":"Adams","year":"1990","journal-title":"J. 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