{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,4,8]],"date-time":"2025-04-08T17:25:55Z","timestamp":1744133155123},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,8,31]],"date-time":"2020-08-31T00:00:00Z","timestamp":1598832000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"EU Horizon 2020 program","award":["643476"],"award-info":[{"award-number":["643476"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,5,17]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The Flavivirus genus includes several important pathogens, such as Zika, dengue and yellow fever virus. Flavivirus RNA genomes contain a number of functionally important structures in their 3\u2032 untranslated regions (3\u2032UTRs). Due to the diversity of sequences and topologies of these structures, their identification is often difficult. In contrast, predictions of such structures are important for understanding of flavivirus replication cycles and development of antiviral strategies.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We have developed an algorithm for structured pattern search in RNA sequences, including secondary structures, pseudoknots and triple base interactions. Using the data on known conserved flavivirus 3\u2032UTR structures, we constructed structural descriptors which covered the diversity of patterns in these motifs. The descriptors and the search algorithm were used for the construction of a database of flavivirus 3\u2032UTR structures. Validating this approach, we identified a number of domains matching a general pattern of exoribonuclease Xrn1-resistant RNAs in the growing group of insect-specific flaviviruses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The Leiden Flavivirus RNA Structure Database is available at https:\/\/rna.liacs.nl. The search algorithm is available at https:\/\/github.com\/LeidenRNA\/SRHS.<\/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\/btaa759","type":"journal-article","created":{"date-parts":[[2020,8,24]],"date-time":"2020-08-24T11:10:38Z","timestamp":1598267438000},"page":"956-962","source":"Crossref","is-referenced-by-count":6,"title":["A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions"],"prefix":"10.1093","volume":"37","author":[{"given":"Alan","family":"Zammit","sequence":"first","affiliation":[{"name":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"}]},{"given":"Leon","family":"Helwerda","sequence":"additional","affiliation":[{"name":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"}]},{"given":"Ren\u00e9 C L","family":"Olsthoorn","sequence":"additional","affiliation":[{"name":"Group Supramolecular & Biomaterials Chemistry, Leiden Institute of Chemistry, Leiden University , 2300 RA Leiden, The Netherlands"}]},{"given":"Fons J","family":"Verbeek","sequence":"additional","affiliation":[{"name":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"}]},{"given":"Alexander P","family":"Gultyaev","sequence":"additional","affiliation":[{"name":"Group Imaging & Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University , 2300 RA Leiden, The Netherlands"},{"name":"Department of Viroscience, Erasmus Medical Center , Rotterdam, 3000 CA, The Netherlands"}]}],"member":"286","published-online":{"date-parts":[[2020,8,31]]},"reference":[{"key":"2023051612174684900_btaa759-B1","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1126\/science.aah3963","article-title":"Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease","volume":"354","author":"Akiyama","year":"2016","journal-title":"Science"},{"key":"2023051612174684900_btaa759-B2","doi-asserted-by":"crossref","first-page":"e6136","DOI":"10.7717\/peerj.6136","article-title":"ScanFold: an approach for genome-wide discovery of local RNA structural elements-applications to Zika virus and HIV","volume":"6","author":"Andrews","year":"2018","journal-title":"PeerJ"},{"key":"2023051612174684900_btaa759-B3","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1261\/rna.1689910","article-title":"Improved free energy parameters for RNA pseudoknotted secondary structure prediction","volume":"16","author":"Andronescu","year":"2010","journal-title":"RNA"},{"key":"2023051612174684900_btaa759-B4","doi-asserted-by":"crossref","first-page":"1927","DOI":"10.3390\/v7041927","article-title":"Insect-specific flaviviruses: a systematic review of their discovery, host range, mode of transmission, superinfection exclusion potential and genomic organization","volume":"7","author":"Blitvich","year":"2015","journal-title":"Viruses"},{"key":"2023051612174684900_btaa759-B5","doi-asserted-by":"crossref","first-page":"i66","DOI":"10.1093\/bioinformatics\/btg1007","article-title":"Stochastic modeling of RNA pseudoknotted structures: a grammatical approach","volume":"19","author":"Cai","year":"2003","journal-title":"Bioinformatics"},{"key":"2023051612174684900_btaa759-B6","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1126\/science.1250897","article-title":"The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production","volume":"344","author":"Chapman","year":"2014","journal-title":"Science"},{"key":"2023051612174684900_btaa759-B7","doi-asserted-by":"crossref","first-page":"e00262","DOI":"10.1128\/mSphere.00262-17","article-title":"A new clade of Insect-specific flaviviruses from Australian Anopheles mosquitoes displays species-specific host restriction","volume":"2","author":"Colmant","year":"2017","journal-title":"mSphere"},{"key":"2023051612174684900_btaa759-B8","doi-asserted-by":"crossref","first-page":"e02506","DOI":"10.1128\/mBio.02506-18","article-title":"RNA structure duplication in the dengue virus 3\u2032 UTR: redundancy or host specificity?","volume":"10","author":"de Borba","year":"2019","journal-title":"mBio"},{"key":"2023051612174684900_btaa759-B9","doi-asserted-by":"crossref","first-page":"405","DOI":"10.4269\/ajtmh.2001.65.405","article-title":"Attenuation and immunogenicity in humans of a live dengue virus type-4 vaccine candidate with a 30 nucleotide deletion in its 3\u2032-untranslated region","volume":"65","author":"Durbin","year":"2001","journal-title":"Am. 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