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Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.

Kerpedjiev P, Hammer S, Hofacker IL - Bioinformatics (2015)

Bottom Line: In this article, we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations.It supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files.It requires no software installation apart from a modern web browser.

View Article: PubMed Central - PubMed

Affiliation: Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and.

No MeSH data available.


Screenshot of forna web app displaying the ‘Bacterial Ribonuclease P Holoenzyme in Complex with tRNA’ (PDB ID: 3Q1Q). Immediately evident are the regions of the tRNA which are in contact with the ribonuclease, namely the 5′ and 3′ end nucleotides, as well as the  loop. An RNA-binding protein is shown as a gray node in the lower-right hand region of the diagram
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btv372-F1: Screenshot of forna web app displaying the ‘Bacterial Ribonuclease P Holoenzyme in Complex with tRNA’ (PDB ID: 3Q1Q). Immediately evident are the regions of the tRNA which are in contact with the ribonuclease, namely the 5′ and 3′ end nucleotides, as well as the loop. An RNA-binding protein is shown as a gray node in the lower-right hand region of the diagram

Mentions: Our tool, called forna (for force-directed rna), consists of a web interface and a server which allows users to input RNA secondary structures as dot-bracket strings, and displays it as a force-directed graph (Screenshot in Fig. 1). In a manner previously demonstrated by jViz.RNA (Wiese etal., 2005) the user can then position each of the nucleotides and stems by dragging them. Each of the nucleotides is represented as a node, whereas backbone and base-pair bonds are considered links. Connections are treated as springs and a force is calculated to keep them a fixed distance from each other. Hidden helper nodes and extra links help to maintain the familiar RNA secondary structure layout. The initial position of each node (nucleotide) is calculated using the NAView algorithm (Bruccoleri and Heinrich, 1988), but is subsequently optimized by the force-directed layout algorithm. This can (especially for larger molecules) lead to artifacts such as twisted helices and nested loops, but these are easily rectified by dragging the affected nodes to their correct positions.Fig. 1.


Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.

Kerpedjiev P, Hammer S, Hofacker IL - Bioinformatics (2015)

Screenshot of forna web app displaying the ‘Bacterial Ribonuclease P Holoenzyme in Complex with tRNA’ (PDB ID: 3Q1Q). Immediately evident are the regions of the tRNA which are in contact with the ribonuclease, namely the 5′ and 3′ end nucleotides, as well as the  loop. An RNA-binding protein is shown as a gray node in the lower-right hand region of the diagram
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595900&req=5

btv372-F1: Screenshot of forna web app displaying the ‘Bacterial Ribonuclease P Holoenzyme in Complex with tRNA’ (PDB ID: 3Q1Q). Immediately evident are the regions of the tRNA which are in contact with the ribonuclease, namely the 5′ and 3′ end nucleotides, as well as the loop. An RNA-binding protein is shown as a gray node in the lower-right hand region of the diagram
Mentions: Our tool, called forna (for force-directed rna), consists of a web interface and a server which allows users to input RNA secondary structures as dot-bracket strings, and displays it as a force-directed graph (Screenshot in Fig. 1). In a manner previously demonstrated by jViz.RNA (Wiese etal., 2005) the user can then position each of the nucleotides and stems by dragging them. Each of the nucleotides is represented as a node, whereas backbone and base-pair bonds are considered links. Connections are treated as springs and a force is calculated to keep them a fixed distance from each other. Hidden helper nodes and extra links help to maintain the familiar RNA secondary structure layout. The initial position of each node (nucleotide) is calculated using the NAView algorithm (Bruccoleri and Heinrich, 1988), but is subsequently optimized by the force-directed layout algorithm. This can (especially for larger molecules) lead to artifacts such as twisted helices and nested loops, but these are easily rectified by dragging the affected nodes to their correct positions.Fig. 1.

Bottom Line: In this article, we present forna, a web-based tool for displaying RNA secondary structure which allows users to easily convert sequences and secondary structures to clean, concise and customizable visualizations.It supports, among other features, the simultaneous visualization of multiple structures, the display of pseudoknotted structures, the interactive editing of the displayed structures, and the automatic generation of secondary structure diagrams from PDB files.It requires no software installation apart from a modern web browser.

View Article: PubMed Central - PubMed

Affiliation: Institute for Theoretical Chemistry, University of Vienna, Währinger Straße 17/3, A-1090 Vienna, Austria and.

No MeSH data available.