{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:40Z","timestamp":1772138080484,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2016,11,10]],"date-time":"2016-11-10T00:00:00Z","timestamp":1478736000000},"content-version":"vor","delay-in-days":73,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004488","name":"Croatian Science Foundation","doi-asserted-by":"publisher","award":["7353"],"award-info":[{"award-number":["7353"]}],"id":[{"id":"10.13039\/501100004488","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Protein database search is one of the fundamental problems in bioinformatics. For decades, it has been explored and solved using different exact and heuristic approaches. However, exponential growth of data in recent years has brought significant challenges in improving already existing algorithms. BLAST has been the most successful tool for protein database search, but is also becoming a bottleneck in many applications. Due to that, many different approaches have been developed to complement or replace it. In this article, we present SWORD, an efficient protein database search implementation that runs 8\u201316 times faster than BLAST in the sensitive mode and up to 68 times faster in the fast and less accurate mode. It is designed to be used in nearly all database search environments, but is especially suitable for large databases. Its sensitivity exceeds that of BLAST for majority of input datasets and provides guaranteed optimal alignments.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Sword is freely available for download from https:\/\/github.com\/rvaser\/sword<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>robert.vaser@fer.hr and mile.sikic@fer.hr<\/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\/btw445","type":"journal-article","created":{"date-parts":[[2016,9,1]],"date-time":"2016-09-01T03:53:39Z","timestamp":1472702019000},"page":"i680-i684","source":"Crossref","is-referenced-by-count":29,"title":["SWORD\u2014a highly efficient protein database search"],"prefix":"10.1093","volume":"32","author":[{"given":"Robert","family":"Vaser","sequence":"first","affiliation":[{"name":"Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia"}]},{"given":"Dario","family":"Pavlovi\u0107","sequence":"additional","affiliation":[{"name":"Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia"}]},{"given":"Mile","family":"\u0160iki\u0107","sequence":"additional","affiliation":[{"name":"Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, Zagreb 10000, Croatia"},{"name":"Bioinformatics Institute, a*STAR, #07-01 Matrix, 138671, Singapore"}]}],"member":"286","published-online":{"date-parts":[[2016,8,29]]},"reference":[{"key":"2023020113282872100_btw445-B1","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1038\/nmeth0410-248","article-title":"A method and server for predicting damaging missense mutations","volume":"7","author":"Adzhubei","year":"2010","journal-title":"Nat. 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