{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T11:31:41Z","timestamp":1740137501330,"version":"3.37.3"},"reference-count":19,"publisher":"World Scientific Pub Co Pte Ltd","issue":"06","funder":[{"DOI":"10.13039\/501100006115","name":"Institute for Research in Fundamental Sciences","doi-asserted-by":"publisher","award":["BS-1394-01-09"],"award-info":[{"award-number":["BS-1394-01-09"]}],"id":[{"id":"10.13039\/501100006115","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2017,12]]},"abstract":"<jats:p> Finding an effective measure to predict a more accurate RNA secondary structure is a challenging problem. In the last decade, an experimental method, known as selective [Formula: see text]-hydroxyl acylation analyzed by primer extension (SHAPE), was proposed to measure the tendency of forming a base pair for almost all nucleotides in an RNA sequence. These SHAPE reactivities are then utilized to improve the accuracy of RNA structure prediction. Due to a significant impact of SHAPE reactivity and in order to reduce the experimental costs, we propose a new model called HL-k-mer. This model simulates the SHAPE reactivity for each nucleotide in an RNA sequence. This is done by fetching the SHAPE reactivities for all sub-sequences of length k (k-mers) appearing in helix and loop regions. For evaluating the quality of simulated SHAPE data, ESD-Fold method is used based on the SHAPE data simulated by the HL-k-mer model ([Formula: see text]). Also, for further evaluation of simulated SHAPE data, three different methods are employed. We also extend this model to simulate the SHAPE data for the RNA pseudoknotted structure. The results indicate that the average accuracies of prediction using the SHAPE data simulated by our models (for [Formula: see text]) are higher compared to the experimental SHAPE data. <\/jats:p>","DOI":"10.1142\/s0219720017500238","type":"journal-article","created":{"date-parts":[[2017,10,19]],"date-time":"2017-10-19T05:14:42Z","timestamp":1508390082000},"page":"1750023","source":"Crossref","is-referenced-by-count":4,"title":["Evaluating the quality of SHAPE data simulated by <i>k-mers<\/i> for RNA structure prediction"],"prefix":"10.1142","volume":"15","author":[{"given":"Soheila","family":"Montaseri","sequence":"first","affiliation":[{"name":"Department of Computer Science, School of Mathematics Statistics, and Computer Science, University of Tehran, Tehran, Iran"}]},{"given":"Fatemeh","family":"Zare-Mirakabad","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Faculty of Mathematics and Computer Science, Amirkabir, University of Technology, Tehran, Iran"}]},{"given":"Mohammad","family":"Ganjtabesh","sequence":"additional","affiliation":[{"name":"Department of Computer Science, School of Mathematics Statistics, and Computer Science, University of Tehran, Tehran, Iran"},{"name":"School of Biological Sciences, Institute for Research in Fundamental Sciences (IPM), Tehran, P.O. Box: 19395-5746, Iran"}]}],"member":"219","published-online":{"date-parts":[[2017,12,12]]},"reference":[{"key":"S0219720017500238BIB001","doi-asserted-by":"publisher","DOI":"10.1137\/0135006"},{"key":"S0219720017500238BIB002","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/9.1.133"},{"key":"S0219720017500238BIB003","doi-asserted-by":"publisher","DOI":"10.1007\/BF00818163"},{"key":"S0219720017500238BIB004","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg595"},{"key":"S0219720017500238BIB005","first-page":"3","volume":"453","author":"Markham NR","year":"2008","journal-title":"Bioinf, Struct Funct Appl"},{"key":"S0219720017500238BIB006","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-11-129"},{"key":"S0219720017500238BIB007","doi-asserted-by":"publisher","DOI":"10.1261\/rna.1166808"},{"key":"S0219720017500238BIB008","doi-asserted-by":"publisher","DOI":"10.1021\/bi200524n"},{"key":"S0219720017500238BIB009","doi-asserted-by":"publisher","DOI":"10.1021\/bi300756s"},{"key":"S0219720017500238BIB010","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2015.05.026"},{"key":"S0219720017500238BIB011","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2010.06.007"},{"key":"S0219720017500238BIB012","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0045160"},{"key":"S0219720017500238BIB013","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1219988110"},{"key":"S0219720017500238BIB014","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1283"},{"key":"S0219720017500238BIB015","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0166965"},{"key":"S0219720017500238BIB016","doi-asserted-by":"publisher","DOI":"10.1021\/bi300755u"},{"key":"S0219720017500238BIB017","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-340"},{"key":"S0219720017500238BIB018","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp892"},{"issue":"2","key":"S0219720017500238BIB019","first-page":"92","volume":"15","author":"Pervouchine DD","year":"2004","journal-title":"Genome Inform"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720017500238","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,21]],"date-time":"2019-09-21T13:46:18Z","timestamp":1569073578000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720017500238"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":19,"journal-issue":{"issue":"06","published-online":{"date-parts":[[2017,12,12]]},"published-print":{"date-parts":[[2017,12]]}},"alternative-id":["10.1142\/S0219720017500238"],"URL":"https:\/\/doi.org\/10.1142\/s0219720017500238","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"type":"print","value":"0219-7200"},{"type":"electronic","value":"1757-6334"}],"subject":[],"published":{"date-parts":[[2017,12]]}}}