RNA Secondary Structure Analysis Using RNAstructure - PubMed (original) (raw)

RNA Secondary Structure Analysis Using RNAstructure

David H Mathews. Curr Protoc Bioinformatics. 2014.

Abstract

RNAstructure is a user-friendly program for the prediction and analysis of RNA secondary structure. It is available as a Web server, as a program with a graphical user interface, or as a set of command-line tools. The programs are available for Microsoft Windows, Macintosh OS X, or Linux. This unit provides protocols for RNA secondary structure prediction (using the Web server or the graphical user interface) and prediction of high-affinity oligonucleotide biding sites to a structured RNA target (using the graphical user interface).

Keywords: RNA secondary structure prediction; free energy minimization; thermodynamics.

PubMed Disclaimer

Cited by

Selection of DNA aptamers that prevent the fibrillization of α-synuclein protein in cellular and mouse models.
McConnell EM, Chan D, Ventura K, Callahan JP, Harris K, Hunt VH, Boisjoli S, Knight D, Monk ET, Holahan MR, DeRosa MC. McConnell EM, et al. Mol Ther Nucleic Acids. 2024 Jun 15;35(3):102251. doi: 10.1016/j.omtn.2024.102251. eCollection 2024 Sep 10. Mol Ther Nucleic Acids. 2024. PMID: 39377064 Free PMC article.
Polyphasic characterization of a novel hot-spring cyanobacterium Thermocoleostomius sinensis gen et sp. nov. and genomic insights into its carbon concentration mechanism.
Jiang Y, Tang J, Liu X, Daroch M. Jiang Y, et al. Front Microbiol. 2023 Jul 26;14:1176500. doi: 10.3389/fmicb.2023.1176500. eCollection 2023. Front Microbiol. 2023. PMID: 37564287 Free PMC article.
In vivo secondary structural analysis of Influenza A virus genomic RNA.
Mirska B, Woźniak T, Lorent D, Ruszkowska A, Peterson JM, Moss WN, Mathews DH, Kierzek R, Kierzek E. Mirska B, et al. Cell Mol Life Sci. 2023 May 2;80(5):136. doi: 10.1007/s00018-023-04764-1. Cell Mol Life Sci. 2023. PMID: 37131079 Free PMC article.
Cooperative engagement and subsequent selective displacement of SR proteins define the pre-mRNA 3D structural scaffold for early spliceosome assembly.
Saha K, Ghosh G. Saha K, et al. Nucleic Acids Res. 2022 Aug 12;50(14):8262-8278. doi: 10.1093/nar/gkac636. Nucleic Acids Res. 2022. PMID: 35871302 Free PMC article.
Polyphasic Identification and Genomic Insights of Leptothermofonsia sichuanensis gen. sp. nov., a Novel Thermophilic Cyanobacteria Within Leptolyngbyaceae.
Tang J, Shah MR, Yao D, Jiang Y, Du L, Zhao K, Li L, Li M, Waleron MM, Waleron M, Waleron K, Daroch M. Tang J, et al. Front Microbiol. 2022 Mar 28;13:765105. doi: 10.3389/fmicb.2022.765105. eCollection 2022. Front Microbiol. 2022. PMID: 35418964 Free PMC article.

References

Literature Cited

References

1. Bellaousov, S. and Mathews, D.H. 2010. ProbKnot: Fast prediction of RNA secondary structure including pseudoknots. RNA 16:1870-1880.
1. Bellaousov, S. , Reuter, J.S. , Seetin, M.G. , and Mathews, D.H. 2013. RNAstructure: Web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res. 41:W471-W474.
1. Bohula, E.A. , Salisbury, A.J. , Sohail, M. , Playford, M.P. , Riedemann, J. , Southern, E.M. , and Macaulay, V.M. 2003. The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem. 278:15991-15997.
1. Brown, J.W. 1999. The ribonuclease P database. Nucleic Acids Res. 27:314.
1. Burgstaller, P. , Hermann, T. , Huber, C. , Westhof, E. , and Famulok, M. 1997. Isoalloxazine derivatives promote photocleavage of natural RNAs at G.U base pairs embedded within helices. Nucleic Acids Res. 25:4018-4027.

RNA Secondary Structure Analysis Using RNAstructure - PubMed (original) (raw)