Result: RNAstructure: software for RNA secondary structure prediction and analysis.
Title:
RNAstructure: software for RNA secondary structure prediction and analysis.
Authors:
Reuter JS; Department of Biochemistry & Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA., Mathews DH
Source:
BMC bioinformatics [BMC Bioinformatics] 2010 Mar 15; Vol. 11, pp. 129. Date of Electronic Publication: 2010 Mar 15.
Publication Type:
Journal Article; Research Support, N.I.H., Extramural
Language:
English
Journal Info:
Publisher: BioMed Central Country of Publication: England NLM ID: 100965194 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2105 (Electronic) Linking ISSN: 14712105 NLM ISO Abbreviation: BMC Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: [London] : BioMed Central, 2000-
MeSH Terms:
References:
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Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102. (PMID: 19109441)
Bioinformatics. 2009 Feb 15;25(4):465-73. (PMID: 19095700)
Curr Opin Cell Biol. 2009 Jun;21(3):359-66. (PMID: 19477626)
Nucleic Acids Res. 2009 Jul;37(12):4063-75. (PMID: 19429694)
Nature. 2009 Aug 6;460(7256):711-6. (PMID: 19661910)
RNA. 2009 Oct;15(10):1805-13. (PMID: 19703939)
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RNA. 2005 Aug;11(8):1157-66. (PMID: 16043502)
BMC Bioinformatics. 2004 Aug 5;5:105. (PMID: 15296519)
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Grant Information:
R01GM076485 United States GM NIGMS NIH HHS
Substance Nomenclature:
63231-63-0 (RNA)
Entry Date(s):
Date Created: 20100317 Date Completed: 20101027 Latest Revision: 20220408
Update Code:
20250114
PubMed Central ID:
PMC2984261
DOI:
10.1186/1471-2105-11-129
PMID:
20230624
Database:
MEDLINE
Further Information
Background: To understand an RNA sequence's mechanism of action, the structure must be known. Furthermore, target RNA structure is an important consideration in the design of small interfering RNAs and antisense DNA oligonucleotides. RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence.
Results: RNAstructure is a software package for RNA secondary structure prediction and analysis. It uses thermodynamics and utilizes the most recent set of nearest neighbor parameters from the Turner group. It includes methods for secondary structure prediction (using several algorithms), prediction of base pair probabilities, bimolecular structure prediction, and prediction of a structure common to two sequences. This contribution describes new extensions to the package, including a library of C++ classes for incorporation into other programs, a user-friendly graphical user interface written in JAVA, and new Unix-style text interfaces. The original graphical user interface for Microsoft Windows is still maintained.
Conclusion: The extensions to RNAstructure serve to make RNA secondary structure prediction user-friendly. The package is available for download from the Mathews lab homepage at http://rna.urmc.rochester.edu/RNAstructure.html.