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Curr Protoc Bioinformatics. 2014 Jun 17;46:12.4.1-22. doi: 10.1002/0471250953.bi1204s46.

Using the RNAstructure Software Package to Predict Conserved RNA Structures.

Author information

1
Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, Rochester, New York.

Abstract

The structures of many non-coding RNA (ncRNA) are conserved by evolution to a greater extent than their sequences. By predicting the conserved structure of two or more homologous sequences, the accuracy of secondary structure prediction can be improved as compared to structure prediction for a single sequence. This unit provides protocols for the use of four programs in the RNAstructure suite for prediction of conserved structures, Multilign, TurboFold, Dynalign, and PARTS. These programs can be run via Web servers, on the command line, or with graphical interfaces.

KEYWORDS:

RNA comparison; RNA folding thermodynamics; RNA secondary structure prediction

PMID:
24939126
PMCID:
PMC4086732
DOI:
10.1002/0471250953.bi1204s46
[Indexed for MEDLINE]
Free PMC Article
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