Journal
NUCLEIC ACIDS RESEARCH
Volume 43, Issue 17, Pages 8135-8145Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkv813
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Funding
- Lundbeck Foundation [R77-A6365, R19-A2306]
- Innovation Fund Denmark [0603-00320B]
- Danish Research Council for independent research [FTP 0602-01096B]
- Danish Center for Scientific Computing (DCSC, DeiC)
- Lundbeck Foundation [R77-2011-6365] Funding Source: researchfish
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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.
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