{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,29]],"date-time":"2026-04-29T15:38:16Z","timestamp":1777477096748,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T00:00:00Z","timestamp":1564617600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,12,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>PRALINE 2 is a toolkit for custom multiple sequence alignment workflows. It can be used to incorporate sequence annotations, such as secondary structure or (DNA) motifs, into the alignment scoring, as well as to customize many other aspects of a progressive multiple alignment workflow.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>PRALINE 2 is implemented in Python and available as open source software on GitHub: https:\/\/github.com\/ibivu\/PRALINE\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz572","type":"journal-article","created":{"date-parts":[[2019,7,29]],"date-time":"2019-07-29T19:11:51Z","timestamp":1564427511000},"page":"5315-5317","source":"Crossref","is-referenced-by-count":4,"title":["Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit"],"prefix":"10.1093","volume":"35","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7971-6209","authenticated-orcid":false,"given":"Maurits J J","family":"Dijkstra","sequence":"first","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit , 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atze J","family":"van der Ploeg","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit , 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"K Anton","family":"Feenstra","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit , 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wan J","family":"Fokkink","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit , 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2779-7174","authenticated-orcid":false,"given":"Sanne","family":"Abeln","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit , 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jaap","family":"Heringa","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Vrije Universiteit , 1081 HV Amsterdam, The Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2019,8,1]]},"reference":[{"key":"2023013108414271600_btz572-B1","doi-asserted-by":"crossref","first-page":"W410","DOI":"10.1093\/nar\/gkw348","article-title":"The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis","volume":"44","author":"Alva","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2023013108414271600_btz572-B2","doi-asserted-by":"crossref","first-page":"e1006547.","DOI":"10.1371\/journal.pcbi.1006547","article-title":"Motif-Aware PRALINE: improving the alignment of motif regions","volume":"14","author":"Dijkstra","year":"2018","journal-title":"PLoS Comput. 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