Search in:

Advanced search

RNA Biology Volume 16, 2019 - Issue 12

Submit an article Journal homepage

Free access

2,456

Views

CrossRef citations to date

Altmetric

Brief Communication

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

Philip Z. JohnsonDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA

https://orcid.org/0000-0002-6689-8306 View further author information

Wojciech K. KasprzakBasic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USAView further author information

Bruce A. ShapiroRNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USAView further author information

Anne E. SimonDepartment of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USACorrespondence[email protected]
View further author information

Pages 1667-1671 | Received 11 Jul 2019, Accepted 20 Aug 2019, Published online: 26 Aug 2019

Cite this article
https://doi.org/10.1080/15476286.2019.1659081
CrossMark

Full Article
Figures & data
References
Citations
Metrics
Reprints & Permissions
View PDF PDF View EPUB EPUB

References

Darty K, Denise A, Ponty Y. VARNA: interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009;25(15):1974–1975.
PubMed Web of Science ®Google Scholar
De Rijk P, Wuyts J, De Wachter R. RnaViz 2: an improved representation of RNA secondary structure. Bioinformatics. 2003;19(2):299–300.
PubMed Web of Science ®Google Scholar
UCSC XRNA. [cited 2019 Aug 19]. http://rna.ucsc.edu/rnacenter/xrna/xrna.html
Google Scholar
Kerpedjiev P, Hammer S, Hofacker IL. Forna (force-directed RNA): simple and effective online RNA secondary structure diagrams. Bioinformatics. 2015;31(20):3377–3379.
PubMed Web of Science ®Google Scholar
Lu JS, Bindewald E, Kasprzak WK, et al. RiboSketch: versatile visualization of multi-stranded RNA and DNA secondary structure. Bioinformatics. 2018;34(24):4297–4299.
PubMed Web of Science ®Google Scholar
Shabash B, Wiese KC. jViz.RNA 4.0-visualizing pseudoknots and RNA editing employing compressed tree graphs. PLoS ONE. 2019;14(5):e0210281.
PubMed Web of Science ®Google Scholar
Bruccoleri RE, Heinrich G. An improved algorithm for nucleic acid secondary structure display. Comput Appl Biosci. 1988;4(1):167–173.
PubMedGoogle Scholar
Shapiro BA, Maizel J, Lipkin LE, et al. Generating non-overlapping displays of nucleic acid secondary structure. Nucleic Acids Res. 1984;12:75–88.
PubMed Web of Science ®Google Scholar
Shapiro BA, Kasprzak W. STRUCTURELAB: a heterogeneous bioinformatics system for RNA structure analysis. J Mol Graph. 1996;14(4):194–205.
PubMedGoogle Scholar
Simon AE. 3’UTRs of carmoviruses. Virus Res. 2015;206:27–36.
PubMed Web of Science ®Google Scholar
Nicholson BL, White KA. Functional long-range RNA-RNA interactions in positive-strand RNA viruses. Nat Rev Microbiol. 2014;12(7):493–504.
PubMed Web of Science ®Google Scholar
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–3415.
PubMed Web of Science ®Google Scholar
Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA. 2001;7(4):499–512.
PubMed Web of Science ®Google Scholar
Wilkinson KA, Merino EJ, Weeks KM. Selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc. 2006;1(3):1610–1616.
PubMed Web of Science ®Google Scholar
Byun Y, Han K. PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. Nucleic Acids Res. 2006;34(Web Server issue):W416–W42.
PubMed Web of Science ®Google Scholar
Elias R, Hoksza D. TRAVeLer: a tool for template-based RNA secondary structure visualization. BMC Bioinformatics. 2017;18(1):487.
PubMed Web of Science ®Google Scholar
Weinberg Z, Breaker RR. R2R–software to speed the depiction of aesthetic consensus RNA secondary structures. BMC Bioinformatics. 2011;12:3.
PubMed Web of Science ®Google Scholar
Jossinet F, Westhof E. Sequence to Structure (S2S): display, manipulate and interconnectRNA data from sequence to structure. Bioinformatics. 2005;21(15):3320–3321.
PubMed Web of Science ®Google Scholar
Jossinet F, Ludwig TE, Westhof E. Assemble: an interactive graphical tool to analyzeand build RNA architectures at the 2D and 3D levels. Bioinformatics. 2010;26(16):2057–2059.
PubMed Web of Science ®Google Scholar

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Order Reprints Request Corporate Permissions

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

Request Academic Permissions

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.

Share icon
Back to Top

Related research

People also read lists articles that other readers of this article have read.

Recommended articles lists articles that we recommend and is powered by our AI driven recommendation engine.

Cited by lists all citing articles based on Crossref citations.
Articles with the Crossref icon will open in a new tab.

People also read
Recommended articles
Cited by

To cite this article:

Reference style: APA Chicago Harvard

Citation copied to clipboard

Reference styles above use APA (6th edition), Chicago (16th edition) & Harvard (10th edition)

Download citation

Download a citation file in RIS format that can be imported by citation management software including EndNote, ProCite, RefWorks and Reference Manager.

Choose format: RIS BibTex RefWorks Direct Export

Choose options: Citation Citation & abstract Citation & references

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

References

Information for

Open access

Opportunities

Help and information

Your download is now in progress and you may close this window

Login or register to access this feature

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

References

Reprints and Corporate Permissions

Academic Permissions

Related research

To cite this article:

Download citation

Information for

Open access

Opportunities

Help and information

Keep up to date