{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T20:12:54Z","timestamp":1775074374440,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"21","license":[{"start":{"date-parts":[[2018,5,16]],"date-time":"2018-05-16T00:00:00Z","timestamp":1526428800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100007156","name":"Hong Kong Innovation and Technology Fund","doi-asserted-by":"crossref","award":["ITS\/155\/15FP"],"award-info":[{"award-number":["ITS\/155\/15FP"]}],"id":[{"id":"10.13039\/501100007156","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Hong Kong ITF","award":["ITS\/155\/15FP"],"award-info":[{"award-number":["ITS\/155\/15FP"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>AC-DIAMOND (v1) is a DNA\u2013protein alignment tool designed to tackle the efficiency challenge of aligning large amount of reads or contigs to protein databases. When compared with the previously most efficient method DIAMOND, AC-DIAMOND gains a 6- to 7-fold speed-up, while retaining a similar degree of sensitivity. The improvement is rooted at two aspects: first, using a compressed index of seeds with adaptive-length to speed-up the matching between query and reference sequences; second, adopting a compact form of dynamic programing to fully utilize the parallelism of the SIMD capability.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Software source codes and binaries available at https:\/\/github.com\/Maihj\/AC-DIAMOND\/<\/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\/bty391","type":"journal-article","created":{"date-parts":[[2018,5,11]],"date-time":"2018-05-11T11:09:25Z","timestamp":1526036965000},"page":"3744-3746","source":"Crossref","is-referenced-by-count":17,"title":["AC-DIAMOND v1: accelerating large-scale DNA\u2013protein alignment"],"prefix":"10.1093","volume":"34","author":[{"given":"Huijun","family":"Mai","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of Hong Kong, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yifan","family":"Zhang","sequence":"additional","affiliation":[{"name":"L3 Bioinformatics Limited, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dinghua","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Hong Kong, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry Chi-Ming","family":"Leung","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Hong Kong, Hong Kong"},{"name":"L3 Bioinformatics Limited, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruibang","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Hong Kong, Hong Kong"},{"name":"L3 Bioinformatics Limited, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chi-Kwong","family":"Wong","sequence":"additional","affiliation":[{"name":"L3 Bioinformatics Limited, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hing-Fung","family":"Ting","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Hong Kong, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tak-Wah","family":"Lam","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of Hong Kong, Hong Kong"},{"name":"L3 Bioinformatics Limited, Hong Kong"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,5,16]]},"reference":[{"key":"2023012712443433400_bty391-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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