Article

Pages 1–2 VARNA: Interactive drawing and editing of the RNA secondary structure

LRI, UMR CNRS 8623, UMR CNRS 8621, Université Paris-Sud 11, F91405 Orsay cedex, France.
Bioinformatics (Impact Factor: 4.98). 05/2009; 25(15):1974-5. DOI: 10.1093/bioinformatics/btp250
Source: PubMed

ABSTRACT

Description: VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases.
Features: VARNA implements four drawing algorithms, supports input/output using the classic formats dbn, ct, bpseq and RNAML and exports the drawing as five picture formats, either pixel-based (JPEG, PNG) or vector-based (SVG, EPS and XFIG). It also allows manual modification and structural annotation of the resulting drawing using either an interactive point and click approach, within a web server or through command-line arguments.
Availability: VARNA is a free software, released under the terms of the GPLv3.0 license and available at http://varna.lri.fr
Contact: ponty@lri.fr
Supplementary information: Supplementary data are available at Bioinformatics online.

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    • "(Nawrocki and Eddy, 2013) cmalign command with an covariance model based on full alignment from (Hooks and Griffiths-Jones, 2011) and then manually adjusted in RALEE (Griffiths-Jones, 2005). Secondary RNA structures were drawn using VARNA (Darty et al., 2009). "
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    • "Possible homology to the ITS2 secondary structure of Gambierdiscus caribaeus (accession number HE775087), available from ITS2-Database version v.5 (Ankenbrand et al. 2015), was explored. Structures were visualized with VARNA (Darty et al. 2009) and then alignment was performed with both 4SALE (Seibel et al. 2006) and ITS2-Database version v.5 (Ankenbrand et al. 2015). Finally, the compensatory and hemi-compensatory base changes (CBC and hemi-CBC) were identified using the software CBCA analyzer (Wolf et al. 2005b). "
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    • "The site where the ASO/siRNA used in this study targets Y3/Y3** is indicated. (B) The depicted secondary structure of Y3** was in silico predicted by RNA fold (University of Vienna) and VARNA (Darty et al. 2009). Note, that studies presented in Figure 4A suggest that the extending U-rich stretch (box) at the Y3**'s 3'-end is essential for the association of CPSF (also see "

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