Literature DB >> 29912310

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

Jacob S Lu1, Eckart Bindewald2, Wojciech K Kasprzak2, Bruce A Shapiro1.   

Abstract

Summary: Creating clear, visually pleasing 2D depictions of RNA and DNA strands and their interactions is important to facilitate and communicate insights related to nucleic acid structure. Here we present RiboSketch, a secondary structure image production application that enables the visualization of multistranded structures via layout algorithms, comprehensive editing capabilities, and a multitude of simulation modes. These interactive features allow RiboSketch to create publication quality diagrams for structures with a wide range of composition, size and complexity. The program may be run in any web browser without the need for installation, or as a standalone Java application. Availability and implementation: https://rnastructure.cancer.gov/ribosketch.

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Year:  2018        PMID: 29912310      PMCID: PMC6289134          DOI: 10.1093/bioinformatics/bty468

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  17 in total

1.  Geometric nomenclature and classification of RNA base pairs.

Authors:  N B Leontis; E Westhof
Journal:  RNA       Date:  2001-04       Impact factor: 4.942

2.  PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots.

Authors:  Yanga Byun; Kyungsook Han
Journal:  Bioinformatics       Date:  2009-04-15       Impact factor: 6.937

3.  RNA secondary structure diagrams for very large molecules: RNAfdl.

Authors:  Nikolai Hecker; Tim Wiegels; Andrew E Torda
Journal:  Bioinformatics       Date:  2013-08-23       Impact factor: 6.937

4.  ViennaRNA Package 2.0.

Authors:  Ronny Lorenz; Stephan H Bernhart; Christian Höner Zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F Stadler; Ivo L Hofacker
Journal:  Algorithms Mol Biol       Date:  2011-11-24       Impact factor: 1.405

5.  DINAMelt web server for nucleic acid melting prediction.

Authors:  Nicholas R Markham; Michael Zuker
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

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

Authors:  Peter Kerpedjiev; Stefan Hammer; Ivo L Hofacker
Journal:  Bioinformatics       Date:  2015-06-22       Impact factor: 6.937

7.  DSSR: an integrated software tool for dissecting the spatial structure of RNA.

Authors:  Xiang-Jun Lu; Harmen J Bussemaker; Wilma K Olson
Journal:  Nucleic Acids Res       Date:  2015-07-15       Impact factor: 16.971

8.  Numerical integration methods and layout improvements in the context of dynamic RNA visualization.

Authors:  Boris Shabash; Kay C Wiese
Journal:  BMC Bioinformatics       Date:  2017-05-30       Impact factor: 3.169

9.  Functionally-interdependent shape-switching nanoparticles with controllable properties.

Authors:  Justin R Halman; Emily Satterwhite; Brandon Roark; Morgan Chandler; Mathias Viard; Anna Ivanina; Eckart Bindewald; Wojciech K Kasprzak; Martin Panigaj; My N Bui; Jacob S Lu; Johann Miller; Emil F Khisamutdinov; Bruce A Shapiro; Marina A Dobrovolskaia; Kirill A Afonin
Journal:  Nucleic Acids Res       Date:  2017-02-28       Impact factor: 16.971

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

Authors:  Richard Elias; David Hoksza
Journal:  BMC Bioinformatics       Date:  2017-11-15       Impact factor: 3.169

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  2 in total

1.  RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences.

Authors:  Philip Z Johnson; Wojciech K Kasprzak; Bruce A Shapiro; Anne E Simon
Journal:  RNA Biol       Date:  2019-08-26       Impact factor: 4.652

Review 2.  Thermostability, Tunability, and Tenacity of RNA as Rubbery Anionic Polymeric Materials in Nanotechnology and Nanomedicine-Specific Cancer Targeting with Undetectable Toxicity.

Authors:  Daniel W Binzel; Xin Li; Nicolas Burns; Eshan Khan; Wen-Jui Lee; Li-Ching Chen; Satheesh Ellipilli; Wayne Miles; Yuan Soon Ho; Peixuan Guo
Journal:  Chem Rev       Date:  2021-05-26       Impact factor: 72.087

  2 in total

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