Local RNA base pairing probabilities in large sequences.
CONCLUSIONS
The genome-wide search for non-coding RNAs requires efficient methods to compute and compare local secondary structures. Since the exact boundaries of such putative transcripts are typically unknown, arbitrary sequence windows have to be used in practice. Here we present a method for robustly computing the probabilities of local base pairs from long RNA sequences independent of the exact positions of the sequence window.


BACKGROUND
The program RNAplfold is part of the Vienna RNA Package and can be downloaded from http://www.tbi.univie.ac.at/RNA/.
Bernhart
Stephan H
SH
Institut für Theoretische Chemie, Universität Wien, Währingerstr. 17, A-1090 Wien, Austria.
Hofacker
Ivo L
IL
Stadler
Peter F
PF
D000465:Algorithms; D020029:Base Pairing / Q000235:genetics*; D002874:Chromosome Mapping / Q000379:methods*; D003198:Computer Simulation; D008957:Models, Genetic; D015233:Models, Statistical; D012313:RNA / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
D012313:RNA