RNApuzzler: efficient outerplanar drawing of RNA-secondary structures

Wiegreffe, Daniel; Alexander, Daniel; Stadler, Peter F.; Zeckzer, Dirk

doi:10.1093/bioinformatics/bty817

Cited by 15 publications

(11 citation statements)

References 18 publications

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“…Then, Elias [24] optimized existing visualization tools based on the corresponding tree that is converted by targets and template structures. Thereafter, to overcome the drawback that some methods cannot always produce intersection-free drawing [25], Wiegreffe proposed an optimization algorithm called RNApuzzler.…”

Section: Related Workmentioning

confidence: 99%

2D Graphical Representation of DNA Sequences Based on Variant Map

Liu

Mao

et al. 2020

IEEE Access

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Mining and analyzing the information and structure of DNA sequences is an important method of exploring and explaining the mysteries of biology. In addition to traditional biological detection methods for DNA sequences, technological advances have allowed researchers to utilize computers to analyze DNA sequences, such as in DNA visualization. However, DNA visualization techniques have disadvantages, such as difficult operation and complex calculation. Therefore, in this paper, we propose an algorithm called VARCH based on a variant map that is a part of variant logic construction. VARCH is a high-efficiency and concise visualization algorithm for DNA sequences. The principle of this approach is that the number of base combinations in each DNA subsequence is counted, and a matrix is constructed based on the full arrangement of different base combinations. Finally, the matrix is mapped to the 2D coordinate plane, obtaining the image of DNA sequences. The experimental results demonstrate that VARCH can effectively display features of DNA sequences.

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Section: Related Workmentioning

confidence: 99%

2D Graphical Representation of DNA Sequences Based on Variant Map

Liu

Mao

et al. 2020

IEEE Access

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“…These structures are represented by RNA secondary structures that can be drawn as planar graphs with some constraints. For example, RNApuzzler [20] uses a similar algorithmic solution to remove overlap by relaxing some constraints; the algorithm recursively checks and solves ancestor and sibling intersections.…”

Section: Related Workmentioning

confidence: 99%

“…Related approaches can also be found in application-specific work. Algorithms that deal with overlap removal are required for Ribonucleic Acid (RNA) structures [1,20]. These structures are represented by RNA secondary structures that can be drawn as planar graphs with some constraints.…”

Section: Related Workmentioning

confidence: 99%

Overlap-Free Drawing of Generalized Pythagoras Trees for Hierarchy Visualization

Munz

Burch

Benthem

et al. 2019

2019 IEEE Visualization Conference (VIS)

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a) Binary tree (e) Self-similar tree (d) Symmetric tree (c) Flat tree (b) Deep treeFigure 1: Comparing the original drawing algorithm of generalized Pythagoras trees (top) to equivalent ones from the suggested overlap-free approach (bottom). The overlap present in the original drawings is completely removed.ABSTRACT Generalized Pythagoras trees were developed for visualizing hierarchical data, producing organic, fractal-like representations. However, the drawback of the original layout algorithm is visual overlap of tree branches. To avoid such overlap, we introduce an adapted drawing algorithm using ellipses instead of circles to recursively place tree nodes representing the subhierarchies. Our technique is demonstrated by resolving overlap in diverse real-world and generated datasets, while comparing the results to the original approach.

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“…Algorithmically, the approaches may use (1) Force-directed layouts where nucleotides represent the nodes of a graph and base pairs as well as other interactions are shown as lines connecting the nodes. These layouts are governed by the attraction and repulsion between the nucleotides and interactions (for example Forna 8 ); or (2) Rule-based methods 9 , such as RNAView 10 , 3DNA 11 , PseudoViewer 12 , R2R 13 , RNA2Drawer 14 , jViz 15 , RNApuzzler 16 and many others, for a more comprehensive review see 17 , 18 . However, none of these methods achieves all five properties of ideal RNA 2D structure diagrams 18 , 19 : they should be modular to reflect functional domains, appear similar for related structures despite sequence or minor structural changes to allow for easy comparison, avoid overlaps and ensure visual clarity, be a realistic representation of the 3D structure (if known), and finally be aesthetically pleasing 18 , 19 .…”

Section: Introductionmentioning

confidence: 99%

“…Specifically, while dot plots are useful for comparative analysis in the hands of expert users 20 , they are difficult for users to interpret; arc plots, which show sequence conservation and base pairs, can be prohibitively large and make it difficult to examine small structural changes; circular diagrams can be uninformative and can make small structural changes hard to analyse; while force-directed layouts are not always robust against changes in the sequence or structure, making a comparison across related structures difficult. The rule-based methods can reliably produce diagrams even for large RNA structures 16 , but they do not take advantage of the community-accepted layouts. In addition, some methods can show other issues such as overlaps and a lack of visual clarity (Fig.…”

Section: Introductionmentioning

confidence: 99%

R2DT is a framework for predicting and visualising RNA secondary structure using templates

et al. 2021

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Non-coding RNAs (ncRNA) are essential for all life, and their functions often depend on their secondary (2D) and tertiary structure. Despite the abundance of software for the visualisation of ncRNAs, few automatically generate consistent and recognisable 2D layouts, which makes it challenging for users to construct, compare and analyse structures. Here, we present R2DT, a method for predicting and visualising a wide range of RNA structures in standardised layouts. R2DT is based on a library of 3,647 templates representing the majority of known structured RNAs. R2DT has been applied to ncRNA sequences from the RNAcentral database and produced >13 million diagrams, creating the world’s largest RNA 2D structure dataset. The software is amenable to community expansion, and is freely available at https://github.com/rnacentral/R2DT and a web server is found at https://rnacentral.org/r2dt.

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RNApuzzler: efficient outerplanar drawing of RNA-secondary structures

Abstract: Supplementary data are available at Bioinformatics online.

Cited by 15 publications

References 18 publications

2D Graphical Representation of DNA Sequences Based on Variant Map

2D Graphical Representation of DNA Sequences Based on Variant Map

Overlap-Free Drawing of Generalized Pythagoras Trees for Hierarchy Visualization

R2DT is a framework for predicting and visualising RNA secondary structure using templates

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