{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T06:31:32Z","timestamp":1762324292979,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2018,6,22]],"date-time":"2018-06-22T00:00:00Z","timestamp":1529625600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Faculty of Electrical, Electronic, Computer and Control Engineering","award":["501\/12-24-1-5418"],"award-info":[{"award-number":["501\/12-24-1-5418"]}]},{"DOI":"10.13039\/501100009894","name":"Lodz University of Technology","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100009894","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100018240","name":"Research Center for Informatics","doi-asserted-by":"crossref","award":["CZ.02.1.01\/0.0\/0.0\/16_019\/0000765"],"award-info":[{"award-number":["CZ.02.1.01\/0.0\/0.0\/16_019\/0000765"]}],"id":[{"id":"10.13039\/100018240","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The many thousands of high-quality genomes available now-a-days imply a shift from single genome to pan-genomic analyses. A basic algorithmic building brick for such a scenario is online search over a collection of similar texts, a problem with surprisingly few solutions presented so far.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present SOPanG, a simple tool for exact pattern matching over an elastic-degenerate string, a recently proposed simplified model for the pan-genome. Thanks to bit-parallelism, it achieves pattern matching speeds above 400 MB\/s, more than an order of magnitude higher than of other software.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SOPanG is available for free from: https:\/\/github.com\/MrAlexSee\/sopang.<\/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\/bty506","type":"journal-article","created":{"date-parts":[[2018,6,20]],"date-time":"2018-06-20T13:22:37Z","timestamp":1529500957000},"page":"4290-4292","source":"Crossref","is-referenced-by-count":14,"title":["SOPanG: online text searching over a pan-genome"],"prefix":"10.1093","volume":"34","author":[{"given":"Aleksander","family":"Cis\u0142ak","sequence":"first","affiliation":[{"name":"Institute of Applied Computer Science, Lodz University of Technology, \u0141\u00f3d\u017a, Poland"}]},{"given":"Szymon","family":"Grabowski","sequence":"additional","affiliation":[{"name":"Institute of Applied Computer Science, Lodz University of Technology, \u0141\u00f3d\u017a, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3022-2694","authenticated-orcid":false,"given":"Jan","family":"Holub","sequence":"additional","affiliation":[{"name":"Faculty of Information Technology, Czech Technical University in Prague, Czechia"}]}],"member":"286","published-online":{"date-parts":[[2018,6,22]]},"reference":[{"key":"2023012712245333900_bty506-B1","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1145\/135239.135243","article-title":"A new approach to text searching","volume":"35","author":"Baeza-Yates","year":"1992","journal-title":"Comm. 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Lett"},{"key":"2023012712245333900_bty506-B5","first-page":"9:1","article-title":"On-line pattern matching on similar texts","volume":"78","author":"Grossi","year":"2017","journal-title":"Proc. CPM. LIPIcs"},{"key":"2023012712245333900_bty506-B6","first-page":"131","article-title":"Efficient pattern matching in elastic-degenerate texts","volume":"10168","author":"Iliopoulos","year":"2017","journal-title":"Proc. LATA. LNCS"},{"key":"2023012712245333900_bty506-B7","first-page":"16:1","volume-title":"Proc. SEA. LIPIcs","author":"Pissis","year":"2018"},{"volume-title":"Algorithms and Data Structures for Sequence Analysis in the Pan-Genomic Era. Ph.D. Dissertation","year":"2017","author":"Valenzuela","key":"2023012712245333900_bty506-B8"},{"key":"2023012712245333900_bty506-B9","first-page":"118","article-title":"Computational pan-genomics: status, promises and challenges","volume":"19","author":"The Computational Pan-Genomics Consortium","year":"2016","journal-title":"Brief. Bioinform"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/24\/4290\/48920191\/bioinformatics_34_24_4290.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/24\/4290\/48920191\/bioinformatics_34_24_4290.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:11:19Z","timestamp":1674825079000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/24\/4290\/5043008"}},"subtitle":[],"editor":[{"given":"Inanc","family":"Birol","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2018,6,22]]},"references-count":9,"journal-issue":{"issue":"24","published-print":{"date-parts":[[2018,12,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty506","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2018,12,15]]},"published":{"date-parts":[[2018,6,22]]}}}