{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T12:59:42Z","timestamp":1761742782855},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but also their potential secondary structures. Sankoff's algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required.<\/jats:p>\n               <jats:p>Results: We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable with the much slower existing algorithms.<\/jats:p>\n               <jats:p>Availability: The web server of SCARNA with graphical structural alignment viewer is available at<\/jats:p>\n               <jats:p>Contact: \u00a0scarna@m.aist.go.jp<\/jats:p>\n               <jats:p>Supplementary information: The data and the supplementary information are available at .<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl177","type":"journal-article","created":{"date-parts":[[2006,5,12]],"date-time":"2006-05-12T07:34:42Z","timestamp":1147419282000},"page":"1723-1729","source":"Crossref","is-referenced-by-count":40,"title":["SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments"],"prefix":"10.1093","volume":"22","author":[{"given":"Yasuo","family":"Tabei","sequence":"first","affiliation":[{"name":"Department of Computational Biology, Graduate School of Frontier Science, University of Tokyo 1 \u00a0 1 \u00a0 \u00a0 CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koji","family":"Tsuda","sequence":"additional","affiliation":[{"name":"Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2 \u00a0 2 \u00a0 \u00a0 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Taishin","family":"Kin","sequence":"additional","affiliation":[{"name":"Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2 \u00a0 2 \u00a0 \u00a0 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kiyoshi","family":"Asai","sequence":"additional","affiliation":[{"name":"Department of Computational Biology, Graduate School of Frontier Science, University of Tokyo 1 \u00a0 1 \u00a0 \u00a0 CB04 Kiban-tou 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan"},{"name":"Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology (AIST) 2 \u00a0 2 \u00a0 \u00a0 2-42 Aomi, Koto-ku, Tokyo, 135-0064, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,5,11]]},"reference":[{"key":"2023012408542185100_b1","first-page":"172","article-title":"Consensus folding of unaligned RNA sequences revisited","author":"Bafna","year":"2005","journal-title":"RECOMB"},{"key":"2023012408542185100_b2","doi-asserted-by":"crossref","first-page":"3497","DOI":"10.1093\/nar\/gkg500","article-title":"Multiple sequence alignment with the clustal series of programs","volume":"31","author":"Chenna","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012408542185100_b3","doi-asserted-by":"crossref","first-page":"919","DOI":"10.1038\/35103511","article-title":"Non-coding RNA genes and the modern RNA world","volume":"2","author":"Eddy","year":"2001","journal-title":"Nat. Genet."},{"key":"2023012408542185100_b4","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012408542185100_b5","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/1471-2105-5-140","article-title":"A comprehensive comparison of comparative RNA structure prediction approaches","volume":"5","author":"Gardner","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012408542185100_b6","doi-asserted-by":"crossref","first-page":"2433","DOI":"10.1093\/nar\/gki541","article-title":"A benchmark of multiple sequence alignment programs upon structural RNAs","volume":"33","author":"Gardner","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408542185100_b7","doi-asserted-by":"crossref","first-page":"823","DOI":"10.1006\/jmbi.1996.0679","article-title":"Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments","volume":"264","author":"Gotoh","year":"1996","journal-title":"J. Mol. Biol."},{"key":"2023012408542185100_b8","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/nar\/gkg006","article-title":"Rfam: an RNA family database","volume":"31","author":"Griffiths-Jones","year":"2003","journal-title":"Nucleic Acids Res."},{"key":"2023012408542185100_b9","doi-asserted-by":"crossref","first-page":"1815","DOI":"10.1093\/bioinformatics\/bti279","article-title":"Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%","volume":"21","author":"Havgaard","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b10","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1007\/BF00818163","article-title":"Fast folding and comparison of RNA secondary structures","volume":"125","author":"Hofacker","year":"1994","journal-title":"Monatsh. Chemie"},{"key":"2023012408542185100_b11","doi-asserted-by":"crossref","first-page":"2222","DOI":"10.1093\/bioinformatics\/bth229","article-title":"Alignment of RNA base pairing probability matrices","volume":"20","author":"Hofacker","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b12","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1016\/S0022-2836(02)00308-X","article-title":"Secondary structure prediction for aligned RNA sequences","volume":"319","author":"Hofacker","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012408542185100_b13","first-page":"163","article-title":"Pairwise RNA structure comparison with stochastic context-free grammars","author":"Holmes","year":"2002","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012408542185100_b14","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1186\/1471-2105-5-166","article-title":"A probabilistic model for the evolution of RNA structure","volume":"5","author":"Holmes","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2023012408542185100_b15","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-6-73","article-title":"Accelerated probabilistic inference of RNA structure evolution","volume":"6","author":"Holmes","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023012408542185100_b16","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1093\/bioinformatics\/bth131","article-title":"A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences","volume":"20","author":"Ji","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b17","first-page":"4","article-title":"Classification of non-coding RNA using graph representations of secondary structure","author":"Karklin","year":"2005","journal-title":"Pac. Symp. Biocomput."},{"key":"2023012408542185100_b18","first-page":"112","article-title":"Marginalized kernels for rna sequence data analysis","volume":"13","author":"Kin","year":"2002","journal-title":"Genome Informatics."},{"key":"2023012408542185100_b19","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2105-4-44","article-title":"RSEARCH: finding homologs of single structured RNA sequences","volume":"4","author":"Klein","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"2023012408542185100_b20","doi-asserted-by":"crossref","first-page":"452","DOI":"10.1093\/bioinformatics\/18.3.452","article-title":"Multiple sequence alignment using partial order graphs","volume":"18","author":"Lee","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b21","doi-asserted-by":"crossref","first-page":"1505","DOI":"10.1093\/bioinformatics\/btg193","article-title":"A hidden Markov model for progressive multiple alignment","volume":"19","author":"Loytynoja","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b22","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1006\/jmbi.2001.5351","article-title":"Dynalign: an algorithm for finding the secondary structure common to two RNA sequences","volume":"317","author":"Mathews","year":"2002","journal-title":"J. Mol. Biol."},{"key":"2023012408542185100_b23","doi-asserted-by":"crossref","first-page":"2246","DOI":"10.1093\/bioinformatics\/bti349","article-title":"Predicting a set of minimal free energy RNA secondary structures common to two sequences","volume":"21","author":"Mathews","year":"2005","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b24","first-page":"442","article-title":"Comparison of the predicted and observed secondary structure of T4 phage lysozyme","volume":"405","author":"Matthews","year":"1975","journal-title":"Biochem. Biophys. Acta"},{"key":"2023012408542185100_b25","doi-asserted-by":"crossref","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":"2023012408542185100_b26","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1137\/0135006","article-title":"Algorithms for loop matchings","volume":"35","author":"Nussinov","year":"1978","journal-title":"SIAM J. App. Math."},{"key":"2023012408542185100_b27","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1093\/bioinformatics\/btg008","article-title":"PCMA: fast and accurate multiple sequence alignment based on profile consistency","volume":"19","author":"Pei","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b28","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1093\/bioinformatics\/19.1.108","article-title":"Finding the common structures shared by two homologous RNAs","volume":"19","author":"Perriquet","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408542185100_b29","doi-asserted-by":"crossref","first-page":"810","DOI":"10.1137\/0145048","article-title":"Simultaneous solution of the RNA folding, alignment, and proto-sequence problems","volume":"45","author":"Sankoff","year":"1985","journal-title":"SIAM J. App. Math."},{"key":"2023012408542185100_b30","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":"2005","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012408542185100_b31","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.jmb.2004.07.018","article-title":"Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics","volume":"342","author":"Washietl","year":"2004","journal-title":"J. Mol. Biol."},{"key":"2023012408542185100_b32","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/nar\/9.1.133","article-title":"Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information","volume":"9","author":"Zuker","year":"1981","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/14\/1723\/48841112\/bioinformatics_22_14_1723.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/14\/1723\/48841112\/bioinformatics_22_14_1723.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:36:36Z","timestamp":1674552996000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/14\/1723\/227337"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,5,11]]},"references-count":32,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2006,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl177","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,7,15]]},"published":{"date-parts":[[2006,5,11]]}}}