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 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.
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.
Nikolai
N
Hecker
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Bledgamsvej 3, 2200 Copenhagen N, Denmark.
Mikkel
M
Christensen-Dalsgaard
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.
Stefan E
SE
Seemann
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark.
Jakob H
JH
Havgaard
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Bioinformatics Group, Department of Computer Science & IZBI-Interdisciplinary Center for Bioinformatics & LIFE-Leipzig Research Center for Civilization Diseases, University Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.
Peter F
PF
Stadler
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria.
Ivo L
IL
Hofacker
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Cellular and Molecular Medicine, Panum Institute, University of Copenhagen, Bledgamsvej 3, 2200 Copenhagen N, Denmark.
Henrik
H
Nielsen
Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark Department of Veterinary Clinical and Animal Science, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark gorodkin@rth.dk.
Jan
J
Gorodkin
D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry*; D059370:RNA Folding; D017423:Sequence Analysis, RNA; D012984:Software
D012313:RNA