{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T04:32:16Z","timestamp":1775190736420,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2024,8,17]],"date-time":"2024-08-17T00:00:00Z","timestamp":1723852800000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,8,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Spaln is the earliest practical tool for self-sufficient genome mapping and spliced alignment of protein query sequences onto a mammalian-sized eukaryotic genomic sequence. However, its computational speed has become inadequate for the analysis of rapidly growing genomic and transcript sequence data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>The dynamic programming calculation of Spaln has been sped up in two ways: (i) the introduction of the multi-intermediate unidirectional Hirschberg method and (ii) SIMD-based vectorization. The new version, Spaln3, is \u223c7 times faster than the latest Spaln version 2, and its gene prediction accuracy is consistently higher than that of Miniprot.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/ogotoh\/spaln.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae517","type":"journal-article","created":{"date-parts":[[2024,8,17]],"date-time":"2024-08-17T14:32:40Z","timestamp":1723905160000},"source":"Crossref","is-referenced-by-count":9,"title":["Spaln3: improvement in speed and accuracy of genome mapping and spliced alignment of protein query sequences"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-6750-1945","authenticated-orcid":false,"given":"Osamu","family":"Gotoh","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Kashiwa, Chiba 277-8562, Japan"},{"name":"Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST) , Koto-ku, Tokyo 135-0064, Japan"}]}],"member":"286","published-online":{"date-parts":[[2024,8,17]]},"reference":[{"key":"2024083002042346600_btae517-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 Mol Biol"},{"key":"2024083002042346600_btae517-B2","doi-asserted-by":"crossref","first-page":"lqaa108","DOI":"10.1093\/nargab\/lqaa108","article-title":"BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database","volume":"3","author":"Br\u016fna","year":"2021","journal-title":"NAR Genom 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