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Improving the accuracy of predicting secondary structure for aligned RNA sequences

Michiaki Hamada, Kengo Sato, Kiyoshi Asai
<span title="2010-09-15">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Considerable attention has been focused on predicting the secondary structure for aligned RNA sequences since it is useful not only for improving the limiting accuracy of conventional secondary structure  ...  Although there exist many algorithms of predicting secondary structure for aligned RNA sequences, further improvement of the accuracy is still awaited.  ...  Frith for commenting on the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq792">doi:10.1093/nar/gkq792</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20843778">pmid:20843778</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3025558/">pmcid:PMC3025558</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lvct5apf5jd2fpp3agf6nkx7ry">fatcat:lvct5apf5jd2fpp3agf6nkx7ry</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226221002/http://pdfs.semanticscholar.org/7808/346796905df36ac43339d949880d9c034e91.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/78/08/7808346796905df36ac43339d949880d9c034e91.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq792"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3025558" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Quantifying variances in comparative RNA secondary structure prediction

James WJ Anderson, Ádám Novák, Zsuzsanna Sükösd, Michael Golden, Preeti Arunapuram, Ingolfur Edvardsson, Jotun Hein
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
The other measure considers the information entropy for SCFGs over a space of input alignments. Conclusions: Our predictive accuracy improves on the PPfold reliability score.  ...  However, current approaches to RNA secondary structure modelling produce predictions with a high variance in predictive accuracy, and we have little quantifiable knowledge about the reasons for these variances  ...  In genome-wide predictions of RNA secondary structure, the accuracy of the secondary structure pre-diction program is rarely factored into analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-14-149">doi:10.1186/1471-2105-14-149</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23634662">pmid:23634662</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3667108/">pmcid:PMC3667108</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xr26lqyodbe5vfiu7jiblatdgi">fatcat:xr26lqyodbe5vfiu7jiblatdgi</a> </span>
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Modeling RNA Secondary Structure with Sequence Comparison and Experimental Mapping Data

Zhen Tan, Gaurav Sharma, David H. Mathews
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dez2wau7t5aqvklzwrcsreuwq4" style="color: black;">Biophysical Journal</a> </i> &nbsp;
Results demonstrate that the SHAPE mapping data for a sequence improves structure prediction accuracy of other homologous sequences beyond the accuracy obtained by sequence comparison alone (TurboFold  ...  Secondary structure prediction is an important problem in RNA bioinformatics because knowledge of structure is critical to understanding the functions of RNA sequences.  ...  ACKNOWLEDGMENTS This work was supported by National Institutes of Health (NIH) grants R01 GM097334 to G.S. and R01 GM076485 to D.H.M.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2017.06.039">doi:10.1016/j.bpj.2017.06.039</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28735622">pmid:28735622</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5529333/">pmcid:PMC5529333</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gue4debyk5f2fp3hbmzuxdt3hm">fatcat:gue4debyk5f2fp3hbmzuxdt3hm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171029170104/http://www.ece.rochester.edu/~gsharma/papers/TanModelRNAStructCompareNExpMap_BiophyJ2017.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/e2/8ae26412f38830d95af3a39194247bb4803bf7ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bpj.2017.06.039"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529333" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

Kazutaka Katoh, Hiroyuki Toh
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler.  ...  Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment.  ...  This work was supported by a Grant-in-Aid for Scientific Research on Priority Areas "Comparative Genomics" from the Ministry of Education, Culture, Sports, Science and Technology of Japan.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-212">doi:10.1186/1471-2105-9-212</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18439255">pmid:18439255</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2387179/">pmcid:PMC2387179</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ng7s44tylzbbdcwlhgx6j364z4">fatcat:ng7s44tylzbbdcwlhgx6j364z4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170822122544/https://link.springer.com/content/pdf/10.1186%2F1471-2105-9-212.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/03/93/0393652ae106dda3bd8730921bfa3c9d06c578b3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-212"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2387179" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai
<span title="2011-05-11">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited.  ...  substantially improved the performance of secondary structure predictions.  ...  In many cases, homologous sequences of the target RNA are available and using those sequences can improve the accuracy of secondary structure predictions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr290">doi:10.1093/nar/gkr290</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21565800">pmid:21565800</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3125741/">pmcid:PMC3125741</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ren5lnxmjraddl4xypmxcldgce">fatcat:ren5lnxmjraddl4xypmxcldgce</a> </span>
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Improving computational efficiency for RNA secondary structure prediction via data-adaptive alignment constraints

Angela D'Orazio, Gaurav Sharma
<span title="">2008</span> <i title="IEEE"> 2008 IEEE International Workshop on Genomic Signal Processing and Statistics </i> &nbsp;
The most accurate methods for RNA secondary structure prediction simultaneously predict the common structure and alignment among multiple homologs.  ...  Our results indicate that we are able to improve runtime with little affect on the accuracy of the structure predictions.  ...  Dynalign simultaneously predicts an alignment and common secondary structure for a pair of sequence by optimizing a cost function [1] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/gensips.2008.4555679">doi:10.1109/gensips.2008.4555679</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3rkonut7enchvpwgxpqhtri4py">fatcat:3rkonut7enchvpwgxpqhtri4py</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150304172439/http://www.ece.rochester.edu/~gsharma/papers/OrazioRNASecStructSpeedupGENSIPS2008.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/52/ed/52ed4da72e3744a3c7e30b918b68d5c55d4d4bd6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/gensips.2008.4555679"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Predicting a set of minimal free energy RNA secondary structures common to two sequences

D. H. Mathews
<span title="2005-02-24">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Results: The Dynalign algorithm, which predicts the lowest free energy secondary structure common to two unaligned RNA sequences, is extended to the prediction of a set of low-energy structures.  ...  Motivation: Function derives from structure, therefore, there is need for methods to predict functional RNA structures.  ...  ACKNOWLEDGEMENTS The author thanks the Rochester Institute of Technology Bioinformatics Program for computer time and three anonymous reviewers for their careful reviews and helpful suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bti349">doi:10.1093/bioinformatics/bti349</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15731207">pmid:15731207</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r3jhdnfd6ncitp3zdfr56gswhi">fatcat:r3jhdnfd6ncitp3zdfr56gswhi</a> </span>
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Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

David H. Mathews, Douglas H. Turner
<span title="">2002</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nk6zopmzsjfizb6z5kztdu477y" style="color: black;">Journal of Molecular Biology</a> </i> &nbsp;
RNA secondary structure prediction for a single sequence is 73 % accurate on average for a large database of known secondary structures.  ...  For the 5 S rRNAs, the average accuracy improves from 47.8 % to 86.4 %. The secondary structure of the R2 3 H UTR from Drosophila takahashii is poorly predicted by standard free energy minimization.  ...  D.H.M. is a trainee in the medical scientist training program, NIH grant 5T32 GM07356  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1006/jmbi.2001.5351">doi:10.1006/jmbi.2001.5351</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11902836">pmid:11902836</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bxwapr2fhbedbb63o7tqw4hew4">fatcat:bxwapr2fhbedbb63o7tqw4hew4</a> </span>
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Multilign: an algorithm to predict secondary structures conserved in multiple RNA sequences

Zhenjiang Xu, David H. Mathews
<span title="2010-12-30">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Multilign was tested on extensive datasets of sequences with known structure and its prediction accuracy is among the best of available algorithms.  ...  In this way, Multilign improves prediction accuracy by keeping the genuine base pairs and excluding competing false base pairs.  ...  ACKNOWLEDGEMENTS The authors thank J.M. Keegan for work on an early prototype of Multilign. Computer time was provided by the University of Rochester Center for Research Computing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq726">doi:10.1093/bioinformatics/btq726</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21193521">pmid:21193521</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3042186/">pmcid:PMC3042186</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wxszujhusfalvbes7vqcvdh76q">fatcat:wxszujhusfalvbes7vqcvdh76q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209213555/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3042186&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9f/1c/9f1c259ed146c78f8a3c6842c22eec20419545be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq726"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042186" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Simultaneous Alignment and Structure Prediction of RNAs [chapter]

Beeta Masoumi, Marcel Turcotte
<span title="">2005</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
Several inference tools are combining free-energy minimisation and comparative analysis to improve the quality of secondary structure predictions.  ...  The following hypotheses were tested: 1) the use of three input sequences improves the average accuracy compared to predictions based on two input sequences.  ...  Availability The source code, written in C++, as well as the scripts for calculating the performance indices are made available under the GNU General Public Licence from http://bio.site.uottawa.ca/software  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11428848_119">doi:10.1007/11428848_119</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nwmdjmlk45aijl7uydwacz5d2i">fatcat:nwmdjmlk45aijl7uydwacz5d2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728023526/https://link.springer.com/content/pdf/10.1007%2F11428848_119.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3d/a2/3da224f0b5a31283cc8447530a47ed61d5a7fcbe.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11428848_119"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Pfold: RNA secondary structure prediction using stochastic context-free grammars

Bjarne Knudsen, Jotun Hein
<span title="2003-07-01">2003</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Many available programs for RNA secondary structure prediction only use a single sequence at a time.  ...  This work presents a practical way of predicting RNA secondary structure that is especially useful when related sequences can be obtained.  ...  The accuracy was calculated as the percentage of positions for which the secondary structure was correctly predicted.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg614">doi:10.1093/nar/gkg614</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12824339">pmid:12824339</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC169020/">pmcid:PMC169020</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2ww7epkrmrasvaw5yb4o7clwo4">fatcat:2ww7epkrmrasvaw5yb4o7clwo4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730015240/https://watermark.silverchair.com/gkg614.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAaAwggGcBgkqhkiG9w0BBwagggGNMIIBiQIBADCCAYIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM0Q9ey8zQeIV2PXvXAgEQgIIBUzCKxM0ZA29NfVl4D4lx-yoGj5VSuogLUA0Cqm6OVRe5f69MsUjv8BOMzc3LxvIImNLz0qbzIJnEJ6w-7-uTtn87_pMfN7WjkUb3iQjfYidtbcZ_eWjU2iv-r3QsKFR_mQUGi0wmyJ5g11YNOGvOXKdSMjfXT_W1GsX_R7kEKmatYUeGOg3AcRu26J4q3BzN9vTp1cjiNjWcf_JkJTX2RtAHFAk_FT1mTo5Iopy1UqcVwoRp4OWBQdmiIFjEokLpu-mQfsBF3_EW28KsgQzvlQqEhKoT6B2_vf21yY-g_oNemw1HWo6sbk6Q_RRMFs-g9_GfTuhnC9-YvtBzT64vAbzKf2OgJCkS_4Ai3aI0HE1s7dJkDRwff1Pj_slTrOR8dF3AEaLXjcFl780dC1jUCtWOPOhAkzutREw-SrXNlftsRo8ik0KDGCw-qD0FAxYben0CGA" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a1/b9/a1b90f6a40d7d0279b4cd6682e8aeeb3ee59374e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkg614"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169020" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Classification System for Predicting RNA Hairpin Loops

Monther Aldwairi, Rehab Duwairi, Wafa'a Alqarqaz
<span title="">2009</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4akrz6fwvzhwrpvtk3vnh7j36q" style="color: black;">2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing</a> </i> &nbsp;
Therefore, computational approaches are used to predict the secondary structure of RNA molecules. A new approach, RNA-SSP, for predicting RNA secondary structure elements is proposed.  ...  The overall weighted-average accuracy for predicting hairpin loop sub-structure is 89% with a sensitivity of 85.29%.  ...  The network of K-nearest neighbor classifiers algorithm (KnetFold), predicts the secondary structure for a set of aligned RNA sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ijcbs.2009.123">doi:10.1109/ijcbs.2009.123</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/ijcbs/AldwairiDA09.html">dblp:conf/ijcbs/AldwairiDA09</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jcl2z5mbonfrjmob2i5dqkivzy">fatcat:jcl2z5mbonfrjmob2i5dqkivzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808211924/http://www.just.edu.jo/~munzer/MyPubs/RNASSP.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/95/19/9519fa057921416c303bed7cf35ee0e7df781a23.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/ijcbs.2009.123"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

Zhen Tan, Yinghan Fu, Gaurav Sharma, David H. Mathews
<span title="2017-09-28">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs.  ...  TurboFold II augments the structure prediction capabilities of Tur-boFold by additionally providing multiple sequence alignments.  ...  As with other structural alignment tools, a limitation of TurboFold II is that its alignment accuracy heavily relies on the accuracy of secondary structure prediction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx815">doi:10.1093/nar/gkx815</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29036420">pmid:29036420</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5714223/">pmcid:PMC5714223</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j3sy2g73izaelefbtzvlav5eba">fatcat:j3sy2g73izaelefbtzvlav5eba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308135248/http://pdfs.semanticscholar.org/e962/ccfd00bed842345ba1fa3cf72f076f16ed5b.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e9/62/e962ccfd00bed842345ba1fa3cf72f076f16ed5b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx815"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5714223" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RNA Secondary Structure Prediction from Multi-Aligned Sequences [chapter]

Michiaki Hamada
<span title="2014-12-16">2014</span> <i title="Springer New York"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6v4flwr6afbfrmhdyu6xe3dyvm" style="color: black;">Msphere</a> </i> &nbsp;
ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome.  ...  In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted.  ...  By employing comparative approaches using homologous sequence information, the accuracy of RNA secondary structure prediction will be improved.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-2291-8_2">doi:10.1007/978-1-4939-2291-8_2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25577370">pmid:25577370</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5txbrogzq5eu7gi2yjk22fewv4">fatcat:5txbrogzq5eu7gi2yjk22fewv4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222124548/http://pdfs.semanticscholar.org/3666/3789ba03880e27dd576f9fd89438bb28769c.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/36/66/36663789ba03880e27dd576f9fd89438bb28769c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-1-4939-2291-8_2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

RNA secondary structure prediction from multi-aligned sequences [article]

Michiaki Hamada
<span title="2013-07-08">2013</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome.  ...  In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted.  ...  By employing comparative approaches using homologous sequence information, the accuracy of RNA secondary structure prediction will be improved.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1307.1934v1">arXiv:1307.1934v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qma53lxhdje5fjjinnscamiitq">fatcat:qma53lxhdje5fjjinnscamiitq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191020123749/https://arxiv.org/pdf/1307.1934v1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/21/d9/21d962ad96f70f4340701e4da6d0be85c74c7960.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1307.1934v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>
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