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Methods Mol Biol. 2016;1490:35-50. doi: 10.1007/978-1-4939-6433-8_3.

Prediction of Secondary Structures Conserved in Multiple RNA Sequences.

Xu ZZ1,2, Mathews DH3,4,5.

Author information

1
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
2
Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA.
3
Department of Biochemistry & Biophysics, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
4
Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.
5
Department of Biostatistics & Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, 712, Rochester, NY, 14642, USA. David_Mathews@urmc.rochester.edu.

Abstract

RNA structure is conserved by evolution to a greater extent than sequence. Predicting the conserved structure for multiple homologous sequences can be much more accurate than predicting the structure for a single sequence. RNAstructure is a software package that includes the programs Dynalign, Multilign, TurboFold, and PARTS for predicting conserved RNA secondary structure. This chapter provides protocols for using these programs.

KEYWORDS:

Comparative sequence analysis; RNA homology; RNA structure prediction

PMID:
27665591
DOI:
10.1007/978-1-4939-6433-8_3
[Indexed for MEDLINE]

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