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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    • "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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    • "Whereas maximum parsimony and neighbor-joining failed in supporting a robust tree topology (besides for the Parachlorella-and the Chlorella-clade), maximum likelihood yielded bootstrap support values N50 for all but one branches (just one terminal clade connecting Micractinium inermum and Hindakia fallax is supported with only 46) (Fig. 6). The 18S tree topology Fig. 3. 5.8S-28S rRNA gene hybridization (proximal stem region) and ITS2 secondary structure of Chlorella vulgaris (AY591505) visualized with VARNA (Darty et al., 2009). The 5.8S is indicated in light gray, the 28S in dark gray. "
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    ABSTRACT: In the last decade, the evolutionary diversity of Chlorella and allies has been discussed in a huge number of publications using internal transcribed spacer 2 (ITS2) and/or 18S ribosomal RNA gene sequences to infer the phylogenies. However, sister-group relations between different genera classified within the Chlorellaceae remained provisional, due to a lack of bootstrap support. In this study, using more than four hundred sequences, a comprehensive phylogenetic portrait of Chlorella and allies is presented and discussed; sixty key taxa are reconsidered by an analysis using primary sequences and their individual secondary structures simultaneously in inferring neighbor-joining, maximum parsimony and maximum likelihood trees, an approach most recently reviewed, with increasing robustness and accuracy of reconstructed phylogenies. While neighbor-joining and maximum parsimony analyses failed in inferring a robust phylogenetic tree, the maximum likelihood tree (in particular on a concatenated data set) provides a supported phylogeny preceding any taxonomic discussion.
    09/2015; 4:20-28. DOI:10.1016/j.plgene.2015.08.001
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    • "The m 6 A modification site (A22 in the oligo or A2577 in MALAT1) is denoted with a red " X " . The figure was made using visualization applet for RNA (VARNA) [30]. (b) Native PAGE (15%) of the unmethylated (M2577-A) and methylated (M2577-m 6 A) hairpins in 25 mM Tris–acetate (pH 7.4) and 2.5 mM magnesium acetate. "
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    ABSTRACT: N6-methyladenosine (m(6)A) is a reversible and abundant internal modification of messenger RNA (mRNA) and long noncoding RNA (lncRNA) with roles in RNA processing, transport, and stability. Although m(6)A does not preclude Watson-Crick base pairing, the N6-methyl group alters the stability of RNA secondary structure. Since changes in RNA structure can affect diverse cellular processes, the influence of m(6)A on mRNA and lncRNA structure has the potential to be an important mechanism for m(6)A function in the cell. Indeed, an m(6)A site in the lncRNA metastasis associated lung adenocarcinoma transcript 1 (MALAT1) was recently shown to induce a local change in structure that increases the accessibility of a U5-tract for recognition and binding by heterogeneous nuclear ribonucleoprotein C (HNRNPC). This m(6)A-dependent regulation of protein binding through a change in RNA structure, termed 'm(6)A-switch,' affects transcriptome-wide mRNA abundance and alternative splicing. To further characterize this first example of an m(6)A-switch in a cellular RNA, we used nuclear magnetic resonance (NMR) and Förster resonance energy transfer (FRET) to demonstrate the effect of m(6)A on a 32-nucleotide RNA hairpin derived from the m(6)A-switch in MALAT1. The observed imino proton NMR resonances and FRET efficiencies suggest that m(6)A selectively destabilizes the portion of the hairpin-stem where the U5-tract is located, increasing the solvent accessibility of the neighboring bases while maintaining the overall hairpin structure. The m(6)A-modified hairpin has a predisposed conformation that resembles the hairpin conformation in the RNA-HNRNPC complex more closely than the unmodified hairpin. The m(6)A-induced structural changes in the MALAT1 hairpin can serve as a model for a large family of m(6)A-switches that mediate the influence of m(6)A on cellular processes.
    Journal of Molecular Biology 09/2015; DOI:10.1016/j.jmb.2015.08.021 · 4.33 Impact Factor
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