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Literature DB >> 24939127

RNA Secondary Structure Analysis Using RNAstructure.

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).

Entities: Chemical

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

Mesh：

Substances：
RNA

Year: 2014 PMID： 24939127 DOI： 10.1002/0471250953.bi1206s46

Source DB: PubMed Journal: Curr Protoc Bioinformatics ISSN： 1934-3396

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Cited

12 in total

1. Human T-cell leukemia virus type 1 Gag domains have distinct RNA-binding specificities with implications for RNA packaging and dimerization.

Authors: Weixin Wu; Joshua Hatterschide; Yu-Ci Syu; William A Cantara; Ruth J Blower; Heather M Hanson; Louis M Mansky; Karin Musier-Forsyth
Journal: J Biol Chem Date: 2018-09-14 Impact factor: 5.157

2. Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.

Authors: Andrew D Kauffmann; Scott D Kennedy; Walter N Moss; Elzbieta Kierzek; Ryszard Kierzek; Douglas H Turner
Journal: RNA Date: 2022-01-04 Impact factor: 4.942

RNA Secondary Structure Analysis Using RNAstructure.

1. Human T-cell leukemia virus type 1 Gag domains have distinct RNA-binding specificities with implications for RNA packaging and dimerization.

2. Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.

3. Inforna 2.0: A Platform for the Sequence-Based Design of Small Molecules Targeting Structured RNAs.

4. A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.

5. Structure of Ty1 Internally Initiated RNA Influences Restriction Factor Expression.

6. Variants in mitochondrial tRNA gene may not be associated with thyroid carcinoma.

7. Metagenomic mining of regulatory elements enables programmable species-selective gene expression.

8. Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment.

9. Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD.

10. A map of the SARS-CoV-2 RNA structurome.