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Methods Mol Biol. 2014;1097:125-41. doi: 10.1007/978-1-62703-709-9_7.

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

Author information

1
Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.

Abstract

Many biologically important RNA structures are conserved in evolution leading to characteristic mutational patterns. RNAalifold is a widely used program to predict consensus secondary structures in multiple alignments by combining evolutionary information with traditional energy-based RNA folding algorithms. Here we describe the theory and applications of the RNAalifold algorithm. Consensus secondary structure prediction not only leads to significantly more accurate structure models, but it also allows to study structural conservation of functional RNAs.

PMID:
24639158
DOI:
10.1007/978-1-62703-709-9_7
[Indexed for MEDLINE]

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