Optimizing RNA structures by sequence extensions using RNAcop

TY - JOUR

T1 - Optimizing RNA structures by sequence extensions using RNAcop

AU - Hecker, Nikolai

AU - Christensen-Dalsgaard, Mikkel

AU - Seemann, Ernst Stefan

AU - Havgaard, Jakob Hull

AU - Stadler, Peter F.

AU - Hofacker, Ivo L

AU - Nielsen, Henrik

AU - Gorodkin, Jan

PY - 2015/9/30

Y1 - 2015/9/30

N2 - 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.

AB - 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.

U2 - 10.1093/nar/gkv813

DO - 10.1093/nar/gkv813

M3 - Journal article

C2 - 26283181

SN - 0305-1048

VL - 43

SP - 8135

EP - 8145

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - 17

ER -