{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T12:06:34Z","timestamp":1785758794692,"version":"3.56.0"},"reference-count":84,"publisher":"PeerJ","license":[{"start":{"date-parts":[[2018,12,18]],"date-time":"2018-12-18T00:00:00Z","timestamp":1545091200000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Iowa State University College of Agriculture and Life Sciences"},{"DOI":"10.13039\/100001024","name":"Roy J. Carver Charitable Trust","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100001024","id-type":"DOI","asserted-by":"crossref"}]},{"name":"NIH\/NIGMS","award":["R00GM112877"],"award-info":[{"award-number":["R00GM112877"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<jats:p>In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions\/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain\u2013Barr\u00e9 syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (<jats:uri xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"https:\/\/www.structurome.bb.iastate.edu\">www.structurome.bb.iastate.edu<\/jats:uri>), a repository of RNA folding data for humans and their pathogens.<\/jats:p>","DOI":"10.7717\/peerj.6136","type":"journal-article","created":{"date-parts":[[2018,12,18]],"date-time":"2018-12-18T09:57:25Z","timestamp":1545127045000},"page":"e6136","source":"Crossref","is-referenced-by-count":95,"title":["ScanFold: an approach for genome-wide discovery of local RNA structural elements\u2014applications to Zika virus and HIV"],"prefix":"10.7717","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0275-0019","authenticated-orcid":true,"given":"Ryan J.","family":"Andrews","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julien","family":"Roche","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6419-5570","authenticated-orcid":true,"given":"Walter N.","family":"Moss","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"4443","published-online":{"date-parts":[[2018,12,18]]},"reference":[{"issue":"6316","key":"10.7717\/peerj.6136\/ref-1","doi-asserted-by":"publisher","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"},{"issue":"6","key":"10.7717\/peerj.6136\/ref-2","doi-asserted-by":"publisher","first-page":"526","DOI":"10.1093\/oxfordjournals.molbev.a040370","article-title":"Significance of nucleotide sequence alignments: a method for random sequence permutation that preserves dinucleotide and codon usage","volume":"2","author":"Altschul","year":"1985","journal-title":"Molecular Biology and Evolution"},{"issue":"11","key":"10.7717\/peerj.6136\/ref-3","doi-asserted-by":"publisher","first-page":"6631","DOI":"10.1128\/JVI.79.11.6631-6643.2005","article-title":"Long-range RNA-RNA interactions circularize the dengue virus genome","volume":"79","author":"Alvarez","year":"2005","journal-title":"Journal of Virology"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-4","doi-asserted-by":"publisher","first-page":"17269","DOI":"10.1038\/s41598-017-17510-y","article-title":"RNAStructuromeDB: A genome-wide database for RNA structural inference","volume":"7","author":"Andrews","year":"2017","journal-title":"Scientific Reports"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-5","doi-asserted-by":"publisher","first-page":"39384","DOI":"10.1038\/srep39384","article-title":"Simple reverse genetics systems for Asian and African Zika viruses","volume":"6","author":"Atieh","year":"2016","journal-title":"Scientific Reports"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-6","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1471-2105-8-33","article-title":"Considerations in the identification of functional RNA structural elements in genomic alignments","volume":"8","author":"Babak","year":"2007","journal-title":"BMC Bioinformatics"},{"issue":"W1","key":"10.7717\/peerj.6136\/ref-7","doi-asserted-by":"publisher","first-page":"W471","DOI":"10.1093\/nar\/gkt290","article-title":"RNAstructure: web servers for RNA secondary structure prediction and analysis","volume":"41","author":"Bellaousov","year":"2013","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-8","doi-asserted-by":"publisher","first-page":"614","DOI":"10.1093\/bioinformatics\/btk014","article-title":"Local RNA base pairing probabilities in large sequences","volume":"22","author":"Bernhart","year":"2006","journal-title":"Bioinformatics"},{"issue":"7","key":"10.7717\/peerj.6136\/ref-9","doi-asserted-by":"publisher","first-page":"1012","DOI":"10.1261\/rna.060194.116","article-title":"Visualization of RNA structure models within the integrative genomics viewer","volume":"23","author":"Busan","year":"2017","journal-title":"RNA"},{"key":"10.7717\/peerj.6136\/ref-10","doi-asserted-by":"publisher","first-page":"e01892","DOI":"10.7554\/eLife.01892","article-title":"RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA","volume":"3","author":"Chapman","year":"2014","journal-title":"Elife"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-11","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1261\/rna.7220505","article-title":"Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency","volume":"11","author":"Clote","year":"2005","journal-title":"RNA"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-12","doi-asserted-by":"publisher","first-page":"e02202-16","DOI":"10.1128\/JVI.02202-16","article-title":"Zika virus methyltransferase: structure and functions for drug design perspectives","volume":"91","author":"Coutard","year":"2017","journal-title":"Journal of Virology"},{"issue":"15","key":"10.7717\/peerj.6136\/ref-13","doi-asserted-by":"publisher","first-page":"1974","DOI":"10.1093\/bioinformatics\/btp250","article-title":"VARNA: interactive drawing and editing of the RNA secondary structure","volume":"25","author":"Darty","year":"2009","journal-title":"Bioinformatics"},{"key":"10.7717\/peerj.6136\/ref-14","doi-asserted-by":"crossref","first-page":"9217","DOI":"10.1128\/JVI.72.11.9217-9223.1998","article-title":"The 5\u2032 and 3\u2032 TAR elements of human immunodeficiency virus exert effects at several points in the virus life cycle","volume":"72","author":"Das","year":"1998","journal-title":"Journal of Virology"},{"issue":"13","key":"10.7717\/peerj.6136\/ref-15","doi-asserted-by":"publisher","first-page":"7622","DOI":"10.1128\/Jvi.00212-13","article-title":"Identification of cis-acting nucleotides and a structural feature in West Nile virus 3\u2032-terminus rna that facilitate viral minus strand RNA synthesis","volume":"87","author":"Davis","year":"2013","journal-title":"Journal of Virology"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-16","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1073\/pnas.0806929106","article-title":"Accurate SHAPE-directed RNA structure determination","volume":"106","author":"Deigan","year":"2009","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7","key":"10.7717\/peerj.6136\/ref-17","doi-asserted-by":"publisher","first-page":"1050","DOI":"10.1038\/nprot.2015.064","article-title":"Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq","volume":"10","author":"Ding","year":"2015","journal-title":"Nature Protocols"},{"issue":"10","key":"10.7717\/peerj.6136\/ref-18","doi-asserted-by":"publisher","first-page":"e0005048","DOI":"10.1371\/journal.pntd.0005048","article-title":"Full genome sequence and sfRNA interferon antagonist activity of Zika virus from Recife, Brazil","volume":"10","author":"Donald","year":"2016","journal-title":"PLOS Neglected Tropical Diseases"},{"issue":"Pt_4","key":"10.7717\/peerj.6136\/ref-19","doi-asserted-by":"publisher","first-page":"763","DOI":"10.1099\/vir.0.062208-0","article-title":"Flavivirus RNA methylation","volume":"95","author":"Dong","year":"2014","journal-title":"Journal of General Virology"},{"issue":"2","key":"10.7717\/peerj.6136\/ref-20","doi-asserted-by":"publisher","first-page":"238","DOI":"10.1016\/j.virol.2004.11.008","article-title":"The majority of the nucleotides in the top loop of the genomic 3\u2032 terminal stem loop structure are cis-acting in a West Nile virus infectious clone","volume":"331","author":"Elghonemy","year":"2005","journal-title":"Virology"},{"issue":"12","key":"10.7717\/peerj.6136\/ref-21","doi-asserted-by":"publisher","first-page":"e1005668","DOI":"10.1371\/journal.pgen.1005668","article-title":"Probing xist RNA structure in cells using targeted structure-seq","volume":"11","author":"Fang","year":"2015","journal-title":"PLOS Genetics"},{"issue":"16","key":"10.7717\/peerj.6136\/ref-22","doi-asserted-by":"publisher","first-page":"2238","DOI":"10.1101\/gad.1444206","article-title":"A 5\u2032 RNA element promotes dengue virus RNA synthesis on a circular genome","volume":"20","author":"Filomatori","year":"2006","journal-title":"Genes & Development"},{"issue":"4","key":"10.7717\/peerj.6136\/ref-23","doi-asserted-by":"publisher","first-page":"745","DOI":"10.1016\/j.jtbi.2007.07.008","article-title":"Calculation of folding energies of single-stranded nucleic acid sequences: conceptual issues","volume":"248","author":"Forsdyke","year":"2007","journal-title":"Journal of Theoretical Biology"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-24","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1186\/1471-2105-6-241","article-title":"A comparison of RNA folding measures","volume":"6","author":"Freyhult","year":"2005","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"10.7717\/peerj.6136\/ref-25","doi-asserted-by":"publisher","first-page":"e0130200","DOI":"10.1371\/journal.pone.0130200","article-title":"Discovery of Novel ncRNA Sequences in Multiple Genome Alignments on the Basis of Conserved and Stable Secondary Structures","volume":"10","author":"Fu","year":"2015","journal-title":"PLOS ONE"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-26","doi-asserted-by":"publisher","first-page":"248","DOI":"10.1186\/1471-2105-9-248","article-title":"Dinucleotide controlled null models for comparative RNA gene prediction","volume":"9","author":"Gesell","year":"2008","journal-title":"BMC Bioinformatics"},{"key":"10.7717\/peerj.6136\/ref-27","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.virusres.2017.08.015","article-title":"Functional RNA during Zika virus infection","volume":"254","author":"Goertz","year":"2017","journal-title":"Virus Research"},{"issue":"22","key":"10.7717\/peerj.6136\/ref-28","doi-asserted-by":"publisher","first-page":"10145","DOI":"10.1128\/Jvi.00930-16","article-title":"Noncoding subgenomic flavivirus RNA is processed by the mosquito RNA interference machinery and determines West Nile virus transmission by culex pipiens mosquitoes","volume":"90","author":"Goertz","year":"2016","journal-title":"Journal of Virology"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-29","doi-asserted-by":"publisher","first-page":"654","DOI":"10.1016\/j.chom.2016.09.015","article-title":"N6-methyladenosine in Flaviviridae viral RNA genomes regulates infection","volume":"20","author":"Gokhale","year":"2016","journal-title":"Cell Host Microbe"},{"key":"10.7717\/peerj.6136\/ref-30","first-page":"69","article-title":"RNAz 2.0: improved noncoding RNA detection","volume":"15","author":"Gruber","year":"2010","journal-title":"Pacific Symposium on Biocomputing"},{"issue":"Suppl_2","key":"10.7717\/peerj.6136\/ref-31","doi-asserted-by":"publisher","first-page":"W335","DOI":"10.1093\/nar\/gkm222","article-title":"The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures","volume":"35","author":"Gruber","year":"2007","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-32","doi-asserted-by":"publisher","first-page":"32713","DOI":"10.1038\/srep32713","article-title":"ZikaVR: an integrated Zika virus resource for genomics, proteomics, phylogenetic and therapeutic analysis","volume":"6","author":"Gupta","year":"2016","journal-title":"Scientific Reports"},{"key":"10.7717\/peerj.6136\/ref-33","doi-asserted-by":"publisher","first-page":"381368","DOI":"10.1101\/381368","article-title":"Structure mapping of dengue and Zika viruses reveals new functional long-range interactions","author":"Huber","year":"2018","journal-title":"bioRxiv preprint"},{"key":"10.7717\/peerj.6136\/ref-34","doi-asserted-by":"publisher","first-page":"e0156906","DOI":"10.1371\/journal.pone.0156906","article-title":"Mutations designed by ensemble defect to misfold conserved RNA structures of influenza a segments 7 and 8 affect splicing and attenuate viral replication in cell culture","volume":"11","author":"Jiang","year":"2016","journal-title":"PLOS ONE"},{"key":"10.7717\/peerj.6136\/ref-35","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbx108","article-title":"MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization","author":"Katoh","year":"2017","journal-title":"Briefings in Bioinformatics"},{"key":"10.7717\/peerj.6136\/ref-36","doi-asserted-by":"publisher","first-page":"44","DOI":"10.3389\/fcimb.2017.00044","article-title":"Mutational pressure in Zika virus: local ADAR-editing areas associated with pauses in translation and replication","volume":"7","author":"Khrustalev","year":"2017","journal-title":"Frontiers in Cellular and Infection Microbiology"},{"issue":"11","key":"10.7717\/peerj.6136\/ref-37","doi-asserted-by":"publisher","first-page":"1169","DOI":"10.1080\/15476286.2015.1094599","article-title":"New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: conservation, folding, and host adaptation","volume":"12","author":"Kieft","year":"2015","journal-title":"RNA Biology"},{"issue":"W1","key":"10.7717\/peerj.6136\/ref-38","doi-asserted-by":"publisher","first-page":"W22","DOI":"10.1093\/nar\/gkt389","article-title":"ALeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity","volume":"41","author":"Kuraku","year":"2013","journal-title":"Nucleic Acids Research"},{"issue":"12","key":"10.7717\/peerj.6136\/ref-39","doi-asserted-by":"publisher","first-page":"5215","DOI":"10.1093\/nar\/gks181","article-title":"Global or local? Predicting secondary structure and accessibility in mRNAs","volume":"40","author":"Lange","year":"2012","journal-title":"Nucleic Acids Research"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-40","doi-asserted-by":"publisher","first-page":"e1004230","DOI":"10.1371\/journal.pcbi.1004230","article-title":"Structure-based alignment and consensus secondary structures for three HIV-related RNA genomes","volume":"11","author":"Lavender","year":"2015","journal-title":"PLOS Computational Biology"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-41","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1016\/j.chom.2016.10.002","article-title":"Dynamics of human and viral RNA methylation during Zika virus infection","volume":"20","author":"Lichinchi","year":"2016","journal-title":"Cell Host & Microbe"},{"key":"10.7717\/peerj.6136\/ref-42","doi-asserted-by":"publisher","first-page":"2582","DOI":"10.3389\/fmicb.2017.02582","article-title":"Know your enemy: successful bioinformatic approaches to predict functional RNA structures in viral RNAs","volume":"8","author":"Lim","year":"2017","journal-title":"Frontiers in Microbiology"},{"issue":"12","key":"10.7717\/peerj.6136\/ref-43","doi-asserted-by":"publisher","first-page":"6804","DOI":"10.1128\/Jvi.00243-13","article-title":"Novel cis-acting element within the capsid-coding region enhances flavivirus viral-RNA replication by regulating genome cyclization","volume":"87","author":"Liu","year":"2013","journal-title":"Journal of Virology"},{"issue":"2","key":"10.7717\/peerj.6136\/ref-44","doi-asserted-by":"publisher","first-page":"993","DOI":"10.1128\/JVI.01647-08","article-title":"Structural and functional studies of the promoter element for dengue virus RNA replication","volume":"83","author":"Lodeiro","year":"2009","journal-title":"Journal of Virology"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-45","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/1748-7188-6-26","article-title":"ViennaRNA Package 2.0","volume":"6","author":"Lorenz","year":"2011","journal-title":"Algorithms for Molecular Biology"},{"key":"10.7717\/peerj.6136\/ref-46","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-1-60327-429-6_1","article-title":"UNAFold: software for nucleic acid folding and hybridization","volume":"453","author":"Markham","year":"2008","journal-title":"Methods in Molecular Biology"},{"issue":"8","key":"10.7717\/peerj.6136\/ref-47","doi-asserted-by":"publisher","first-page":"1178","DOI":"10.1261\/rna.7650904","article-title":"Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization","volume":"10","author":"Mathews","year":"2004","journal-title":"RNA"},{"issue":"19","key":"10.7717\/peerj.6136\/ref-48","doi-asserted-by":"publisher","first-page":"7287","DOI":"10.1073\/pnas.0401799101","article-title":"Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure","volume":"101","author":"Mathews","year":"2004","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"12","key":"10.7717\/peerj.6136\/ref-49","doi-asserted-by":"publisher","first-page":"a003665","DOI":"10.1101\/cshperspect.a003665","article-title":"Folding and finding RNA secondary structure","volume":"2","author":"Mathews","year":"2010","journal-title":"Cold Spring Harbor Perspectives in Biology"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-50","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1006\/jmbi.1999.2700","article-title":"Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure","volume":"288","author":"Mathews","year":"1999","journal-title":"Journal of Molecular Biology"},{"issue":"6\u20137","key":"10.7717\/peerj.6136\/ref-51","doi-asserted-by":"publisher","first-page":"1105","DOI":"10.1002\/bip.360290621","article-title":"The equilibrium partition function and base pair binding probabilities for RNA secondary structure","volume":"29","author":"McCaskill","year":"1990","journal-title":"Biopolymers"},{"key":"10.7717\/peerj.6136\/ref-52","doi-asserted-by":"publisher","first-page":"275","DOI":"10.1002\/9780470559277.ch120019","article-title":"SHAPE-seq: high-throughput RNA structure analysis","volume":"4","author":"Mortimer","year":"2012","journal-title":"Current Protocols in Chemical Biology"},{"issue":"3","key":"10.7717\/peerj.6136\/ref-53","doi-asserted-by":"publisher","first-page":"273","DOI":"10.1261\/rna.063933.117","article-title":"RNA2DMut: a web tool for the design and analysis of RNA structure mutations","volume":"24","author":"Moss","year":"2018","journal-title":"RNA"},{"issue":"6","key":"10.7717\/peerj.6136\/ref-54","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1261\/rna.2619511","article-title":"Identification of potential conserved RNA secondary structure throughout influenza a coding regions","volume":"17","author":"Moss","year":"2011","journal-title":"RNA"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-55","doi-asserted-by":"publisher","first-page":"543","DOI":"10.1186\/1471-2164-14-543","article-title":"Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA","volume":"14","author":"Moss","year":"2013","journal-title":"BMC Genomics"},{"issue":"7","key":"10.7717\/peerj.6136\/ref-56","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1038\/nrmicro3288","article-title":"Functional long-range RNA\u2013RNA interactions in positive-strand RNA viruses","volume":"12","author":"Nicholson","year":"2014","journal-title":"Nature Reviews Microbiology"},{"issue":"7","key":"10.7717\/peerj.6136\/ref-57","doi-asserted-by":"publisher","first-page":"2353","DOI":"10.1093\/nar\/gkn076","article-title":"Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element","volume":"36","author":"Ouellet","year":"2008","journal-title":"Nucleic Acids Research"},{"issue":"6","key":"10.7717\/peerj.6136\/ref-58","doi-asserted-by":"publisher","first-page":"579","DOI":"10.1016\/j.chom.2008.10.007","article-title":"A highly structured, nuclease-resistant, noncoding RNA produced by flaviviruses is required for pathogenicity","volume":"4","author":"Pijlman","year":"2008","journal-title":"Cell Host & Microbe"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-59","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1016\/j.ceb.2012.08.015","article-title":"Taking a cellular road-trip: mRNA transport and anchoring","volume":"25","author":"Pratt","year":"2013","journal-title":"Current Opinion in Cell Biology"},{"issue":"8","key":"10.7717\/peerj.6136\/ref-60","doi-asserted-by":"publisher","first-page":"5403","DOI":"10.1093\/nar\/gku208","article-title":"CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction","volume":"42","author":"Puton","year":"2014","journal-title":"Nucleic Acids Research"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-61","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1186\/1471-2105-11-129","article-title":"RNAstructure: software for RNA secondary structure prediction and analysis","volume":"11","author":"Reuter","year":"2010","journal-title":"BMC Bioinformatics"},{"issue":"14","key":"10.7717\/peerj.6136\/ref-62","doi-asserted-by":"publisher","first-page":"e135","DOI":"10.1093\/nar\/gkx533","article-title":"Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo","volume":"45","author":"Ritchey","year":"2017","journal-title":"Nucleic Acids Research"},{"issue":"2","key":"10.7717\/peerj.6136\/ref-63","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1016\/j.bpj.2016.12.037","article-title":"Opportunities and challenges in RNA structural modeling and design","volume":"113","author":"Schlick","year":"2017","journal-title":"Biophysical Journal"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-64","doi-asserted-by":"publisher","first-page":"2891","DOI":"10.1128\/JVI.03014-13","article-title":"Identifying recombination hot spots in the HIV-1 genome","volume":"88","author":"Smyth","year":"2014","journal-title":"Journal of Virology"},{"issue":"2","key":"10.7717\/peerj.6136\/ref-65","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/s10867-013-9313-0","article-title":"Packaging signals in single-stranded RNA viruses: nature\u2019s alternative to a purely electrostatic assembly mechanism","volume":"39","author":"Stockley","year":"2013","journal-title":"Journal of Biological Physics"},{"issue":"8","key":"10.7717\/peerj.6136\/ref-66","doi-asserted-by":"publisher","first-page":"392","DOI":"10.3390\/genes9080392","article-title":"RNA structure elements conserved between mouse and 59 other vertebrates","volume":"9","author":"Thiel","year":"2018","journal-title":"Genes"},{"issue":"2","key":"10.7717\/peerj.6136\/ref-67","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1093\/bib\/bbs017","article-title":"Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration","volume":"14","author":"Thorvaldsdottir","year":"2013","journal-title":"Briefings in Bioinformatics"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-68","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1099\/vir.0.19462-0","article-title":"Conserved RNA secondary structures in Flaviviridae genomes","volume":"85","author":"Thurner","year":"2004","journal-title":"Journal of General Virology"},{"issue":"12","key":"10.7717\/peerj.6136\/ref-69","doi-asserted-by":"publisher","first-page":"2325","DOI":"10.1261\/rna.2120410","article-title":"A balance between circular and linear forms of the dengue virus genome is crucial for viral replication","volume":"16","author":"Villordo","year":"2010","journal-title":"RNA"},{"issue":"4","key":"10.7717\/peerj.6136\/ref-70","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1016\/j.tim.2016.01.002","article-title":"RNA structure duplications and flavivirus host adaptation","volume":"24","author":"Villordo","year":"2016","journal-title":"Trends in Microbiology"},{"key":"10.7717\/peerj.6136\/ref-71","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1007\/978-1-59745-514-5_32","article-title":"Prediction of structural noncoding RNAs with RNAz","volume":"395","author":"Washietl","year":"2007","journal-title":"Methods in Molecular Biology"},{"issue":"11","key":"10.7717\/peerj.6136\/ref-72","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1038\/nbt1144","article-title":"Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome","volume":"23","author":"Washietl","year":"2005a","journal-title":"Nature Biotechnology"},{"key":"10.7717\/peerj.6136\/ref-73","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1073\/pnas.0409169102","article-title":"Fast and reliable prediction of noncoding RNAs","volume":"102","author":"Washietl","year":"2005b","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"10","key":"10.7717\/peerj.6136\/ref-74","doi-asserted-by":"publisher","first-page":"4261","DOI":"10.1093\/nar\/gks009","article-title":"RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction","volume":"40","author":"Washietl","year":"2012","journal-title":"Nucleic Acids Research"},{"issue":"7256","key":"10.7717\/peerj.6136\/ref-75","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/nature08237","article-title":"Architecture and secondary structure of an entire HIV-1 RNA genome","volume":"460","author":"Watts","year":"2009","journal-title":"Nature"},{"issue":"4","key":"10.7717\/peerj.6136\/ref-76","doi-asserted-by":"publisher","first-page":"e96","DOI":"10.1371\/journal.pbio.0060096","article-title":"High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states","volume":"6","author":"Wilkinson","year":"2008","journal-title":"PLOS Biology"},{"issue":"3","key":"10.7717\/peerj.6136\/ref-77","doi-asserted-by":"publisher","first-page":"1610","DOI":"10.1038\/nprot.2006.249","article-title":"Selective 2\u2032-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution","volume":"1","author":"Wilkinson","year":"2006","journal-title":"Nature Protocols"},{"issue":"5","key":"10.7717\/peerj.6136\/ref-78","doi-asserted-by":"publisher","first-page":"900","DOI":"10.1261\/rna.029041.111","article-title":"LocARNA-P: accurate boundary prediction and improved detection of structural RNAs","volume":"18","author":"Will","year":"2012","journal-title":"RNA"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-79","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1006\/viro.1998.9589","article-title":"Interactions between Tat and TAR and human immunodeficiency virus replication are facilitated by human cyclin T1 but not cyclins T2a or T2b","volume":"255","author":"Wimmer","year":"1999","journal-title":"Virology"},{"issue":"1","key":"10.7717\/peerj.6136\/ref-80","doi-asserted-by":"publisher","first-page":"10","DOI":"10.1016\/j.gene.2012.03.021","article-title":"The regulation of mRNA stability in mammalian cells: 2.0","volume":"500","author":"Wu","year":"2012","journal-title":"Gene"},{"key":"10.7717\/peerj.6136\/ref-81","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1016\/j.meegid.2016.05.004","article-title":"Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas","volume":"43","author":"Ye","year":"2016","journal-title":"Infection, Genetics and Evolution"},{"issue":"4","key":"10.7717\/peerj.6136\/ref-82","doi-asserted-by":"publisher","first-page":"2309","DOI":"10.1128\/Jvi.79.4.2309-2324.2005","article-title":"The topology of bulges in the long stem of the flavivirus 3\u2032 stem-loop is a major determinant of RNA replication competence","volume":"79","author":"Yu","year":"2005","journal-title":"Journal of Virology"},{"issue":"10","key":"10.7717\/peerj.6136\/ref-83","doi-asserted-by":"publisher","first-page":"e45160","DOI":"10.1371\/journal.pone.0045160","article-title":"Integrating chemical footprinting data into RNA secondary structure prediction","volume":"7","author":"Zarringhalam","year":"2012","journal-title":"PLOS ONE"},{"key":"10.7717\/peerj.6136\/ref-84","doi-asserted-by":"crossref","first-page":"7510","DOI":"10.1128\/JVI.72.9.7510-7522.1998","article-title":"Identification of specific nucleotide sequences within the conserved 3\u2032-SL in the dengue type 2 virus genome required for replication","volume":"72","author":"Zeng","year":"1998","journal-title":"Journal of Virology"}],"container-title":["PeerJ"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/peerj.com\/articles\/6136.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/6136.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/6136.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/peerj.com\/articles\/6136.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,18]],"date-time":"2020-11-18T02:55:47Z","timestamp":1605668147000},"score":1,"resource":{"primary":{"URL":"https:\/\/peerj.com\/articles\/6136"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12,18]]},"references-count":84,"alternative-id":["10.7717\/peerj.6136"],"URL":"https:\/\/doi.org\/10.7717\/peerj.6136","archive":["CLOCKSS","LOCKSS","Portico"],"relation":{},"ISSN":["2167-8359"],"issn-type":[{"value":"2167-8359","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12,18]]},"article-number":"e6136"}}