{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:04:38Z","timestamp":1773270278251,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"6","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2013,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: We have developed essaMEM, a tool for finding maximal exact matches that can be used in genome comparison and read mapping. essaMEM enhances an existing sparse suffix array implementation with a sparse child array. Tests indicate that the enhanced algorithm for finding maximal exact matches is much faster, while maintaining the same memory footprint. In this way, sparse suffix arrays remain competitive with the more complex compressed suffix arrays.<\/jats:p>\n               <jats:p>Availability: Source code is freely available at https:\/\/github.ugent.be\/ComputationalBiology\/essaMEM.<\/jats:p>\n               <jats:p>Contact: \u00a0Michael.Vyverman@UGent.be<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btt042","type":"journal-article","created":{"date-parts":[[2013,1,25]],"date-time":"2013-01-25T01:49:00Z","timestamp":1359078540000},"page":"802-804","source":"Crossref","is-referenced-by-count":45,"title":["essaMEM: finding maximal exact matches using enhanced sparse suffix arrays"],"prefix":"10.1093","volume":"29","author":[{"given":"Micha\u00ebl","family":"Vyverman","sequence":"first","affiliation":[{"name":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"}]},{"given":"Bernard","family":"De Baets","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"}]},{"given":"Veerle","family":"Fack","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"}]},{"given":"Peter","family":"Dawyndt","sequence":"additional","affiliation":[{"name":"1 Department of Applied Mathematics and Computer Science and 2Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent B-9000, Belgium"}]}],"member":"286","published-online":{"date-parts":[[2013,1,24]]},"reference":[{"key":"2023012810291020700_btt042-B1","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/S1570-8667(03)00065-0","article-title":"Replacing suffix trees with enhanced suffix arrays","volume":"2","author":"Abouelhoda","year":"2004","journal-title":"J. Discrete Algorithms"},{"key":"2023012810291020700_btt042-B2","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1007\/3-540-45452-7_13","article-title":"Space-economical algorithms for finding maximal unique matches","volume-title":"Proceedings of the Annual Symposium on Combinatorial Pattern Matching","author":"Hon","year":"2002"},{"key":"2023012810291020700_btt042-B3","doi-asserted-by":"crossref","first-page":"1609","DOI":"10.1093\/bioinformatics\/btp275","article-title":"A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays","volume":"25","author":"Khan","year":"2009","journal-title":"Bioinformatics"},{"key":"2023012810291020700_btt042-B4","doi-asserted-by":"crossref","first-page":"R12","DOI":"10.1186\/gb-2004-5-2-r12","article-title":"Versatile and open software for comparing large genomes","volume":"5","author":"Kurtz","year":"2004","journal-title":"Genome Biol."},{"key":"2023012810291020700_btt042-B5","doi-asserted-by":"crossref","DOI":"10.1145\/1216370.1216372","article-title":"Compressed full-text indexes","volume":"39","author":"Navarro","year":"2007","journal-title":"ACM Comput. Surv."},{"key":"2023012810291020700_btt042-B6","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1007\/978-3-642-16321-0_36","article-title":"Computing matching statistics and maximal exact matches on compressed full-text indexes","volume-title":"Proceedings of the 17th Annual Symposium on String Processing and Information Retrieval","author":"Ohlebusch","year":"2010"},{"key":"2023012810291020700_btt042-B7","doi-asserted-by":"crossref","first-page":"6993","DOI":"10.1093\/nar\/gks408","article-title":"Prospects and limitations of full-text index structures in genome analysis","volume":"40","author":"Vyverman","year":"2012","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/6\/802\/48898765\/bioinformatics_29_6_802.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/29\/6\/802\/48898765\/bioinformatics_29_6_802.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,28]],"date-time":"2023-01-28T10:29:27Z","timestamp":1674901767000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/29\/6\/802\/184020"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,24]]},"references-count":7,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2013,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btt042","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2013,3,15]]},"published":{"date-parts":[[2013,1,24]]}}}