{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T16:42:48Z","timestamp":1779381768365,"version":"3.53.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2016,10,12]],"date-time":"2016-10-12T00:00:00Z","timestamp":1476230400000},"content-version":"vor","delay-in-days":293,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and are local in their genomic or transcriptomic context. Thus, the need for tools which in particular can make local structural alignments of RNAs is only increasing.<\/jats:p>\n               <jats:p>Results: To meet the demand for both large-scale screens and hands on analysis through web servers, we present a new multithreaded version of Foldalign. We substantially improve execution time while maintaining all previous functionalities, including carrying out local structural alignments of sequences with low similarity. Furthermore, the improvements allow for comparing longer RNAs and increasing the sequence length. For example, lengths in the range 2000\u20136000 nucleotides improve execution up to a factor of five.<\/jats:p>\n               <jats:p>Availability and implementation: The Foldalign software and the web server are available at http:\/\/rth.dk\/resources\/foldalign<\/jats:p>\n               <jats:p>Contact: \u00a0gorodkin@rth.dk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv748","type":"journal-article","created":{"date-parts":[[2015,12,25]],"date-time":"2015-12-25T03:13:42Z","timestamp":1451013222000},"page":"1238-1240","source":"Crossref","is-referenced-by-count":38,"title":["Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment"],"prefix":"10.1093","volume":"32","author":[{"given":"Daniel","family":"Sundfeld","sequence":"first","affiliation":[{"name":"1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and"},{"name":"2 Department of Computer Science, University of Brasilia, Bras\u00edlia, DF, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jakob H.","family":"Havgaard","sequence":"additional","affiliation":[{"name":"1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alba C. 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A.","family":"de Melo","sequence":"additional","affiliation":[{"name":"2 Department of Computer Science, University of Brasilia, Bras\u00edlia, DF, Brazil"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Gorodkin","sequence":"additional","affiliation":[{"name":"1 Center for Non-Coding RNA in Technology and Health, IKVH, University of Copenhagen, Frederiksberg, Denmark and"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2015,12,24]]},"reference":[{"key":"2023020112203628600_btv748-B1","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1186\/1471-2105-7-400","article-title":"Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints","volume":"7","author":"Dowell","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"2023020112203628600_btv748-B2","doi-asserted-by":"crossref","first-page":"13939","DOI":"10.1093\/nar\/gku1172","article-title":"Dynalign II: common secondary structure prediction for RNA homologs with domain insertions","volume":"42","author":"Fu","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023020112203628600_btv748-B3","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.tibtech.2009.09.006","article-title":"De novo prediction of structured RNAs from genomic sequences","volume":"28","author":"Gorodkin","year":"2010","journal-title":"Trends Biotechnol"},{"key":"2023020112203628600_btv748-B4","doi-asserted-by":"crossref","first-page":"1896","DOI":"10.1371\/journal.pcbi.0030193","article-title":"Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix","volume":"3","author":"Havgaard","year":"2007","journal-title":"PLoS Comput. 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