{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T08:21:25Z","timestamp":1759134085749},"reference-count":19,"publisher":"Association for Computing Machinery (ACM)","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proc. VLDB Endow."],"published-print":{"date-parts":[[2011,9]]},"abstract":"<jats:p>The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix tree are too large to fit into the main memory, most existing construction algorithms become very inefficient.<\/jats:p>\n          <jats:p>This paper presents a disk-based suffix tree construction method, called Elastic Range (ERa), which works efficiently with very long strings that are much larger than the available memory. ERa partitions the tree construction process horizontally and vertically and minimizes I\/Os by dynamically adjusting the horizontal partitions independently for each vertical partition, based on the evolving shape of the tree and the available memory. Where appropriate, ERa also groups vertical partitions together to amortize the I\/O cost. We developed a serial version; a parallel version for shared-memory and shared-disk multi-core systems; and a parallel version for shared-nothing architectures. ERa indexes the entire human genome in 19 minutes on an ordinary desktop computer. For comparison, the fastest existing method needs 15 minutes using 1024 CPUs on an IBM BlueGene supercomputer.<\/jats:p>","DOI":"10.14778\/2047485.2047490","type":"journal-article","created":{"date-parts":[[2014,6,24]],"date-time":"2014-06-24T12:17:57Z","timestamp":1403612277000},"page":"49-60","source":"Crossref","is-referenced-by-count":45,"title":["ERA"],"prefix":"10.14778","volume":"5","author":[{"given":"Essam","family":"Mansour","sequence":"first","affiliation":[{"name":"King Abdullah Univ. of Science and Technology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amin","family":"Allam","sequence":"additional","affiliation":[{"name":"King Abdullah Univ. of Science and Technology"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Spiros","family":"Skiadopoulos","sequence":"additional","affiliation":[{"name":"University of Peloponnese"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Panos","family":"Kalnis","sequence":"additional","affiliation":[{"name":"King Abdullah Univ. of Science and Technology"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2011,9]]},"reference":[{"key":"e_1_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1145\/1240233.1240242"},{"key":"e_1_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1145\/1645953.1646134"},{"key":"e_1_2_1_3_1","volume-title":"Handbook of Exact String Matching Algorithms","author":"Charras C.","year":"2004","unstructured":"C. Charras and T. Lecroq . Handbook of Exact String Matching Algorithms . King's College London Publications , 2004 . C. Charras and T. Lecroq. Handbook of Exact String Matching Algorithms. King's College London Publications, 2004."},{"key":"e_1_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1145\/1242572.1242590"},{"key":"e_1_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1145\/1082036.1082043"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1145\/1654059.1654122"},{"key":"e_1_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1145\/1559845.1559931"},{"key":"e_1_2_1_8_1","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511574931","volume-title":"Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology","author":"Gusfield D.","year":"1997","unstructured":"D. Gusfield . Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology . Cambridge University Press , 1997 . D. Gusfield. 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