{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,13]],"date-time":"2026-03-13T08:24:06Z","timestamp":1773390246268,"version":"3.50.1"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2019,7,11]],"date-time":"2019-07-11T00:00:00Z","timestamp":1562803200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001602","name":"Science Foundation Ireland","doi-asserted-by":"publisher","award":["11\/PI\/1034"],"award-info":[{"award-number":["11\/PI\/1034"]}],"id":[{"id":"10.13039\/501100001602","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Secondary structure prediction accuracy (SSPA) in the QuanTest benchmark can be used to measure accuracy of a multiple sequence alignment. SSPA correlates well with the sum-of-pairs score, if the results are averaged over many alignments but not on an alignment-by-alignment basis. This is due to a sub-optimal selection of reference and non-reference sequences in QuanTest.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We develop an improved strategy for selecting reference and non-reference sequences for a new benchmark, QuanTest2. In QuanTest2, SSPA and SP correlate better on an alignment-by-alignment basis than in QuanTest. Guide-trees for QuanTest2 are more balanced with respect to reference sequences than in QuanTest. QuanTest2 scores correlate well with other well-established benchmarks.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>QuanTest2 is available at http:\/\/bioinf.ucd.ie\/quantest2.tar, comprises of reference and non-reference sequence sets and a scoring script.<\/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\/btz552","type":"journal-article","created":{"date-parts":[[2019,7,9]],"date-time":"2019-07-09T15:10:39Z","timestamp":1562685039000},"page":"90-95","source":"Crossref","is-referenced-by-count":19,"title":["QuanTest2: benchmarking multiple sequence alignments using secondary structure prediction"],"prefix":"10.1093","volume":"36","author":[{"given":"Fabian","family":"Sievers","sequence":"first","affiliation":[{"name":"Conway Institute, UCD School of Medicine, University College Dublin , Belfield, Dublin 4, Ireland"}]},{"given":"Desmond G","family":"Higgins","sequence":"additional","affiliation":[{"name":"Conway Institute, UCD School of Medicine, University College Dublin , Belfield, Dublin 4, Ireland"}]}],"member":"286","published-online":{"date-parts":[[2019,7,11]]},"reference":[{"key":"2023013109500376400_btz552-B1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1007\/978-1-62703-646-7_16","article-title":"PRALINE: a versatile multiple sequence alignment toolkit","volume":"1079","author":"Bawono","year":"2014","journal-title":"Methods Mol. 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