Optimizing RNA structures by sequence extensions using RNAcop

A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences...

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Main Authors:	Hecker, Nikolai, Christensen-Dalsgaard, Mikkel, Seemann, Stefan E., Havgaard, Jakob H., Stadler, Peter F., Hofacker, Ivo L., Nielsen, Henrik, Gorodkin, Jan
Format:	Online
Language:	English
Published:	Oxford University Press 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787817/

id	pubmed-4787817
recordtype	oai_dc
spelling	pubmed-47878172016-03-14 Optimizing RNA structures by sequence extensions using RNAcop Hecker, Nikolai Christensen-Dalsgaard, Mikkel Seemann, Stefan E. Havgaard, Jakob H. Stadler, Peter F. Hofacker, Ivo L. Nielsen, Henrik Gorodkin, Jan Computational Biology A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop. Oxford University Press 2015-09-30 2015-08-17 /pmc/articles/PMC4787817/ /pubmed/26283181 http://dx.doi.org/10.1093/nar/gkv813 Text en © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Hecker, Nikolai Christensen-Dalsgaard, Mikkel Seemann, Stefan E. Havgaard, Jakob H. Stadler, Peter F. Hofacker, Ivo L. Nielsen, Henrik Gorodkin, Jan
spellingShingle	Hecker, Nikolai Christensen-Dalsgaard, Mikkel Seemann, Stefan E. Havgaard, Jakob H. Stadler, Peter F. Hofacker, Ivo L. Nielsen, Henrik Gorodkin, Jan Optimizing RNA structures by sequence extensions using RNAcop
author_facet	Hecker, Nikolai Christensen-Dalsgaard, Mikkel Seemann, Stefan E. Havgaard, Jakob H. Stadler, Peter F. Hofacker, Ivo L. Nielsen, Henrik Gorodkin, Jan
author_sort	Hecker, Nikolai
title	Optimizing RNA structures by sequence extensions using RNAcop
title_short	Optimizing RNA structures by sequence extensions using RNAcop
title_full	Optimizing RNA structures by sequence extensions using RNAcop
title_fullStr	Optimizing RNA structures by sequence extensions using RNAcop
title_full_unstemmed	Optimizing RNA structures by sequence extensions using RNAcop
title_sort	optimizing rna structures by sequence extensions using rnacop
description	A key aspect of RNA secondary structure prediction is the identification of novel functional elements. This is a challenging task because these elements typically are embedded in longer transcripts where the borders between the element and flanking regions have to be defined. The flanking sequences impact the folding of the functional elements both at the level of computational analyses and when the element is extracted as a transcript for experimental analysis. Here, we analyze how different flanking region lengths impact folding into a constrained structure by computing probabilities of folding for different sizes of flanking regions. Our method, RNAcop (RNA context optimization by probability), is tested on known and de novo predicted structures. In vitro experiments support the computational analysis and suggest that for a number of structures, choosing proper lengths of flanking regions is critical. RNAcop is available as web server and stand-alone software via http://rth.dk/resources/rnacop.
publisher	Oxford University Press
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4787817/
_version_	1613550642330075136

Optimizing RNA structures by sequence extensions using RNAcop

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