RNA Secondary Structure Diagrams for Very Large Molecules: RNAfdl

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2013 Aug 27

PMID 23975766

Citations 7

Authors

Nikolai Hecker

Tim Wiegels

Andrew E Torda

Affiliations

Soon will be listed here.

Abstract

Summary: There are many programs that can read the secondary structure of an RNA molecule and draw a diagram, but hardly any that can cope with 10(3) bases. RNAfdl is slow but capable of producing intersection-free diagrams for ribosome-sized structures, has a graphical user interface for adjustments and produces output in common formats.

Availability And Implementation: Source code is available under the GNU General Public License v3.0 at http://sourceforge.net/projects/rnafdl for Linux and similar systems or Windows using MinGW. RNAfdl is implemented in C, uses the Cairo 2D graphics library and offers both command line and graphical user interfaces.

Contact: hecker@rth.dk

Citing Articles

R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions.

Tsybulskyi V, Mounir M, Meyer I Nucleic Acids Res. 2020; 48(18):e105.

PMID: 32976561 PMC: 7544209. DOI: 10.1093/nar/gkaa708.

RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure.

Lu J, Bindewald E, Kasprzak W, Shapiro B Bioinformatics. 2018; 34(24):4297-4299.

PMID: 29912310 PMC: 6289134. DOI: 10.1093/bioinformatics/bty468.

TRAVeLer: a tool for template-based RNA secondary structure visualization.

Elias R, Hoksza D BMC Bioinformatics. 2017; 18(1):487.

PMID: 29141608 PMC: 5688744. DOI: 10.1186/s12859-017-1885-4.

Associating transcription factors and conserved RNA structures with gene regulation in the human brain.

Hecker N, Seemann S, Silahtaroglu A, Ruzzo W, Gorodkin J Sci Rep. 2017; 7(1):5776.

PMID: 28720872 PMC: 5516038. DOI: 10.1038/s41598-017-06200-4.

JNSViewer-A JavaScript-based Nucleotide Sequence Viewer for DNA/RNA secondary structures.

Shi J, Li X, Dong M, Graham M, Yadav N, Liang C PLoS One. 2017; 12(6):e0179040.

PMID: 28582416 PMC: 5459502. DOI: 10.1371/journal.pone.0179040.