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


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
Supplementary information: Supplementary data are available at Bioinformatics online.

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Available from: Yann Ponty
    • "(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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    ABSTRACT: Honey bee colonies in the United States have suffered from an increased rate of die-off in recent years, stemming from a complex set of interacting stresses that remain poorly described. While we have some understanding of the physiological stress responses in the honey bee, our molecular understanding of honey bee cellular stress responses is incomplete. Thus, we sought to identify and began functional characterization of the components of the UPR in honey bees. The IRE1-dependent splicing of the mRNA for the transcription factor Xbp1, leading to translation of an isoform with more transactivation potential, represents the most conserved of the UPR pathways. Honey bees and other Apoidea possess unique features in the Xbp1 mRNA splice site, which we reasoned could have functional consequences for the IRE1 pathway. However, we find robust induction of target genes upon UPR stimulation. In addition, the IRE1 pathway activation, as assessed by splicing of Xbp1 mRNA upon UPR, is conserved. By providing foundational knowledge about the UPR in the honey bee and the relative sensitivity of this species to divergent stresses, this work stands to improve our understanding of the mechanistic underpinnings of honey bee health and disease.
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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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    ABSTRACT: A single cell of the dinoflagellate genus Fukuyoa was isolated from the island of Formentera (Balearic Islands, west Mediterranean Sea), cultured and characterized by morphological and molecular methods and toxin analyses. This is the first report of the Gambierdiscus lineage (genera Fukuyoa and Gambierdiscus) from the western Mediterranean Sea, which is cooler than its eastern basin. Molecular analyses revealed that the Mediterranean strain belongs to F. paulensis, and that it bears LSU rDNA sequences identical to New Zealand, Australian and Brazilian strains. It also shared an identical sequence of the more variable ITS-rDNA with the Brazilian strain. Toxin analyses showed the presence of maitotoxin, 54-deoxyCTX1B and gambieric acid A. This is the first observation of the two latter compounds in a Fukuyoa strain. Therefore, both Gambierdiscus and Fukuyoa should be considered when as contributing to ciguatera fish poisoning. Different strains of Fukuyoa form a complex of morphologically cryptic lineages where F. paulensis stands as the most distantly related nominal species. The comparison of the ITS2 secondary structures revealed the absence of CBCs among strains. The study of the morphological and molecular traits depicted an unresolved taxonomic scenario impacted by the low strains sampling. This article is protected by copyright. All rights reserved.
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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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