{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,6,4]],"date-time":"2024-06-04T04:29:00Z","timestamp":1717475340088},"reference-count":27,"publisher":"Hindawi Limited","license":[{"start":{"date-parts":[[2010,9,16]],"date-time":"2010-09-16T00:00:00Z","timestamp":1284595200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/3.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Advances in Bioinformatics"],"published-print":{"date-parts":[[2010,9,16]]},"abstract":"<jats:p>The advent of high-throughput sequencing technologies constituted\na major advance in genomic studies, offering new prospects in a\nwide range of applications.We propose a rigorous and flexible algorithmic\nsolution to mapping SOLiD color-space reads to a reference genome. The\nsolution relies on an advanced method of seed design that uses a faithful\nprobabilistic model of read matches and, on the other hand, a novel\nseeding principle especially adapted to read mapping. Our method can\nhandle both lossy and lossless frameworks and is able to distinguish, at\nthe level of seed design, between SNPs and reading errors. We illustrate\nour approach by several seed designs and demonstrate their efficiency.<\/jats:p>","DOI":"10.1155\/2010\/708501","type":"journal-article","created":{"date-parts":[[2010,9,16]],"date-time":"2010-09-16T17:36:23Z","timestamp":1284658583000},"page":"1-12","source":"Crossref","is-referenced-by-count":3,"title":["Designing Efficient Spaced Seeds for SOLiD Read Mapping"],"prefix":"10.1155","volume":"2010","author":[{"given":"Laurent","family":"No\u00e9","sequence":"first","affiliation":[{"name":"INRIA Lille-Nord Europe, LIFL\/CNRS, Universit\u00e9 Lille 1, 59655 Villeneuve d'Ascq, France"}]},{"given":"Marta","family":"G\u00eerdea","sequence":"additional","affiliation":[{"name":"INRIA Lille-Nord Europe, LIFL\/CNRS, Universit\u00e9 Lille 1, 59655 Villeneuve d'Ascq, France"}]},{"given":"Gregory","family":"Kucherov","sequence":"additional","affiliation":[{"name":"INRIA Lille-Nord Europe, LIFL\/CNRS, Universit\u00e9 Lille 1, 59655 Villeneuve d'Ascq, France"},{"name":"J.-V.Poncelet Laboratory, Bolshoy Vlasyevsky 11, Moscow 119002, Russia"}]}],"member":"98","reference":[{"issue":"3","key":"1","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1093\/bioinformatics\/18.3.440","volume":"18","year":"2002","journal-title":"Bioinformatics"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gki478"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1101\/gr.078212.108"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp087"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp486"},{"key":"8","doi-asserted-by":"publisher","DOI":"10.1101\/gr.088823.108"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000386"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn416"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2009-10-3-r25"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp324"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btp336"},{"key":"14","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000502"},{"key":"15","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0007767"},{"key":"16","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn512"},{"key":"17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btn223"},{"key":"18","doi-asserted-by":"publisher","DOI":"10.1038\/nature07517"},{"key":"19","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2005.12"},{"key":"20","doi-asserted-by":"publisher","DOI":"10.1142\/S0219720006001977"},{"issue":"3","key":"23","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1101\/gr.8.3.186","volume":"8","year":"1998","journal-title":"Genome Research"},{"key":"24","doi-asserted-by":"publisher","DOI":"10.1142\/S0219720004000661"},{"key":"25","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2005.12.847"},{"key":"27","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-36"},{"key":"28","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2007.0209"},{"key":"32","doi-asserted-by":"publisher","DOI":"10.1016\/S0166-218X(03)00382-2"},{"issue":"1-2","key":"34","first-page":"51","volume":"56","year":"2003","journal-title":"Fundamenta Informaticae"},{"key":"35","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl263"},{"issue":"3","key":"37","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1016\/0022-2836(82)90398-9","volume":"162","year":"1982","journal-title":"Journal of Molecular Biology"}],"container-title":["Advances in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/708501.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/708501.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/archive\/2010\/708501.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,12,9]],"date-time":"2020-12-09T00:02:02Z","timestamp":1607472122000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/abi\/2010\/708501\/"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,9,16]]},"references-count":27,"alternative-id":["708501","708501"],"URL":"https:\/\/doi.org\/10.1155\/2010\/708501","relation":{},"ISSN":["1687-8027","1687-8035"],"issn-type":[{"value":"1687-8027","type":"print"},{"value":"1687-8035","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,9,16]]}}}