{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T00:43:06Z","timestamp":1778632986517,"version":"3.51.4"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2016,11,26]],"date-time":"2016-11-26T00:00:00Z","timestamp":1480118400000},"content-version":"vor","delay-in-days":57,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Health and Medical Research","award":["12110542"],"award-info":[{"award-number":["12110542"]}]},{"name":"RGC Collaborative Research","award":["CUHK3\/CRF\/11G"],"award-info":[{"award-number":["CUHK3\/CRF\/11G"]}]},{"name":"RGC Collaborative Research","award":["C4042-14G"],"award-info":[{"award-number":["C4042-14G"]}]},{"name":"Theme-based research schemes","award":["T12-403\/11"],"award-info":[{"award-number":["T12-403\/11"]}]},{"name":"Theme-based research schemes","award":["T12-401\/13R"],"award-info":[{"award-number":["T12-401\/13R"]}]},{"name":"Theme-based research schemes","award":["T12-402\/13-N"],"award-info":[{"award-number":["T12-402\/13-N"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Optical mapping is a technique for capturing fluorescent signal patterns of long DNA molecules (in the range of 0.1\u20131 Mbp). Recently, it has been complementing the widely used short-read sequencing technology by assisting with scaffolding and detecting large and complex structural variations (SVs). Here, we introduce a fast, robust and accurate tool called OMBlast for aligning optical maps, the set of signal locations on the molecules generated from optical mapping. Our method is based on the seed-and-extend approach from sequence alignment, with modifications specific to optical mapping.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Experiments with both synthetic and our real data demonstrate that OMBlast has higher accuracy and faster mapping speed than existing alignment methods. Our tool also shows significant improvement when aligning data with SVs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>OMBlast is implemented for Java 1.7 and is released under a GPL license. OMBlast can be downloaded from https:\/\/github.com\/aldenleung\/OMBlast and run directly on machines equipped with a Java virtual machine.<\/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\/btw620","type":"journal-article","created":{"date-parts":[[2016,9,29]],"date-time":"2016-09-29T19:06:19Z","timestamp":1475175979000},"page":"311-319","source":"Crossref","is-referenced-by-count":35,"title":["OMBlast: alignment tool for optical mapping using a seed-and-extend approach"],"prefix":"10.1093","volume":"33","author":[{"given":"Alden King-Yung","family":"Leung","sequence":"first","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tsz-Piu","family":"Kwok","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raymond","family":"Wan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ming","family":"Xiao","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, Science and Health System, Drexel University, Philadelphia, PA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pui-Yan","family":"Kwok","sequence":"additional","affiliation":[{"name":"Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA"},{"name":"Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kevin Y","family":"Yip","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ting-Fung","family":"Chan","sequence":"additional","affiliation":[{"name":"School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Hong Kong, China"},{"name":"Centre for Soybean Research, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,9,30]]},"reference":[{"key":"2023020204405196100_btw620-B1","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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