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

Kerpedjiev, Peter; Hammer, Stefan; Hofacker, Ivo L.

doi:10.1093/bioinformatics/btv372

Cited by 370 publications

(283 citation statements)

References 7 publications

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“…(a) Due to the Watson-Crick base pair mechanism and neglecting the difference of excluded volumes between loops and stems, single filaments of RNA have a branched secondary structure (here, visualized by the FORNA 31 software). These structures have been shown 6–8 to play a crucial functional role in the RNA behavior inside viral capsids.…”

Section: Figmentioning

confidence: 99%

Flory theory of randomly branched polymers

et al. 2017

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Randomly branched polymer chains (or trees) are a classical subject of polymer physics with connections to the theory of magnetic systems, percolation and critical phenomena. More recently, the model has been reconsidered for RNA, supercoiled DNA and the crumpling of topologically-constrained polymers. While solvable in the ideal case, little is known exactly about randomly branched polymers with volume interactions. Flory theory provides a simple, unifying description for a wide range of branched systems, including isolated trees in good and θ-solvent, and tree melts. In particular, the approach provides a common framework for the description of randomly branched polymers with quenched connectivity and for randomly branching polymers with annealed connectivity. Here we review the Flory theory for interacting trees in the asymptotic limit of very large polymerization degree for good solvent, θ-solutions and melts, and report its predictions for annealed connectivity in θ-solvents. We compare the predictions of Flory theory for randomly branched polymers to a wide range of available analytical and numerical results and conclude that they are qualitatively excellent and quantitatively good in most cases.

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Section: Figmentioning

confidence: 99%

Flory theory of randomly branched polymers

et al. 2017

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“…In addition, users can also find the sequence and structural motifs of the binding sites of a given RBP. (iii) The ‘Structure’ visualization mode provides local RNA secondary structure visualization (78) for every RBP binding site. Previous studies suggest that RNA secondary structures can provide specific binding sites for RBPs and restrict protein binding by altering structural accessibility (79,80).…”

Section: Database Features and Applicationsmentioning

confidence: 99%

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

et al. 2016

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We present POSTAR (http://POSTAR.ncrnalab.org), a resource of POST-trAnscriptional Regulation coordinated by RNA-binding proteins (RBPs). Precise characterization of post-transcriptional regulatory maps has accelerated dramatically in the past few years. Based on new studies and resources, POSTAR supplies the largest collection of experimentally probed (∼23 million) and computationally predicted (approximately 117 million) RBP binding sites in the human and mouse transcriptomes. POSTAR annotates every transcript and its RBP binding sites using extensive information regarding various molecular regulatory events (e.g., splicing, editing, and modification), RNA secondary structures, disease-associated variants, and gene expression and function. Moreover, POSTAR provides a friendly, multi-mode, integrated search interface, which helps users to connect multiple RBP binding sites with post-transcriptional regulatory events, phenotypes, and diseases. Based on our platform, we were able to obtain novel insights into post-transcriptional regulation, such as the putative association between CPSF6 binding, RNA structural domains, and Li-Fraumeni syndrome SNPs. In summary, POSTAR represents an early effort to systematically annotate post-transcriptional regulatory maps and explore the putative roles of RBPs in human diseases.

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“…1D) and structure diagrams (Fig. 1E) generated using the ViennaRNA package (Hofacker, 2013; Kerpedjiev et al , 2015, Lorenz et al , 2011). The corresponding MFE structures can be downloaded as tab-delimited text files.…”

Section: Resultsmentioning

confidence: 99%

FoldAtlas: a repository for genome-wide RNA structure probing data

et al. 2016

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SummaryMost RNA molecules form internal base pairs, leading to a folded secondary structure. Some of these structures have been demonstrated to be functionally significant. High-throughput RNA structure chemical probing methods generate millions of sequencing reads to provide structural constraints for RNA secondary structure prediction. At present, processed data from these experiments are difficult to access without computational expertise. Here we present FoldAtlas, a web interface for accessing raw and processed structural data across thousands of transcripts. FoldAtlas allows a researcher to easily locate, view, and retrieve probing data for a given RNA molecule. We also provide in silico and in vivo secondary structure predictions for comparison, visualized in the browser as circle plots and topology diagrams. Data currently integrated into FoldAtlas are from a new high-depth Structure-seq data analysis in Arabidopsis thaliana, released with this work.Availability and ImplementationThe FoldAtlas website can be accessed at www.foldatlas.com. Source code is freely available at github.com/mnori/foldatlas under the MIT license. Raw reads data are available under the NCBI SRA accession SRP066985.Supplementary information Supplementary data are available at Bioinformatics online.

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

Cited by 370 publications

References 7 publications

Flory theory of randomly branched polymers

Flory theory of randomly branched polymers

POSTAR: a platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins

FoldAtlas: a repository for genome-wide RNA structure probing data

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