jViz.Rna —A Java Tool for RNA Secondary Structure Visualization

Wiese, Kay C.; Glen, Edward; Vasudevan, Alexander

doi:10.1109/tnb.2005.853646

Cited by 49 publications

(39 citation statements)

References 11 publications

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“…This folding method creates secondary structures based on multiple sequences. The output from KnetFold was entered into jViz.RNA 2.0 in order to visualize the secondary structure (49). jViz.RNA 2.0 allows for the creation of complex 2°s tructures that may contain pseudoknots.…”

Section: Methodsmentioning

confidence: 99%

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei

Oberdorf²,

Nossa³

et al. 2010

Appl Environ Microbiol

242

181

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Analysis of intragenomic variation of 16S rRNA genes is a unique approach to examining the concept of ribosomal constraints on rRNA genes; the degree of variation is an important parameter to consider for estimation of the diversity of a complex microbiome in the recently initiated Human Microbiome Project (http://nihroadmap.nih.gov/hmp). The current GenBank database has a collection of 883 prokaryotic genomes representing 568 unique species, of which 425 species contained 2 to 15 copies of 16S rRNA genes per genome (2.22 ؎ 0.81). Sequence diversity among the 16S rRNA genes in a genome was found in 235 species (from 0.06% to 20.38%; 0.55% ؎ 1.46%). Compared with the 16S rRNA-based threshold for operational definition of species (1 to 1.3% diversity), the diversity was borderline (between 1% and 1.3%) in 10 species and >1.3% in 14 species. The diversified 16S rRNA genes in Haloarcula marismortui (diversity, 5.63%) and Thermoanaerobacter tengcongensis (6.70%) were highly conserved at the 2°structure level, while the diversified gene in B. afzelii (20.38%) appears to be a pseudogene. The diversified genes in the remaining 21 species were also conserved, except for a truncated 16S rRNA gene in "Candidatus Protochlamydia amoebophila." Thus, this survey of intragenomic diversity of 16S rRNA genes provides strong evidence supporting the theory of ribosomal constraint. Taxonomic classification using the 16S rRNA-based operational threshold could misclassify a number of species into more than one species, leading to an overestimation of the diversity of a complex microbiome. This phenomenon is especially seen in 7 bacterial species associated with the human microbiome or diseases.

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Section: Methodsmentioning

confidence: 99%

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Pei

Oberdorf²,

Nossa³

et al. 2010

Appl Environ Microbiol

242

181

View full text Add to dashboard Cite

show abstract

“…For the convenience of end-users, the FASTR webserver also provides download links for (a) various dependencies of the FASTR program viz. JRE, RNAfold program (b) tools for inter-converting between various RNA secondary structure file formats (Wiese et al 2005;Lorenz et al 2011;Antczak et al 2014), and (c) other nucleotide sequence archival tools like DSRC (Deorowicz and Grabowski 2011), DELIMINATE , BIND , MFCompress (Pinho and Pratas 2014) and FQC (Dutta et al 2015).…”

Section: Discussionmentioning

confidence: 99%

FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information

Bose

Dutta

et al. 2015

J Biosci

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Given the importance of RNA secondary structures in defining their biological role, it would be convenient for researchers seeking RNA data if both sequence and structural information pertaining to RNA molecules are made available together. Current nucleotide data repositories archive only RNA sequence data. Furthermore, storage formats which can frugally represent RNA sequence as well as structure data in a single file, are currently unavailable. This article proposes a novel storage format, 'FASTR', for concomitant representation of RNA sequence and structure. The storage efficiency of the proposed FASTR format has been evaluated using RNA data from various microorganisms. Results indicate that the size of FASTR formatted files (containing both RNA sequence as well as structure information) are equivalent to that of FASTA-format files, which contain only RNA sequence information. RNA secondary structure is typically represented using a combination of a string of nucleotide characters along with the corresponding dot-bracket notation indicating structural attributes. 'FASTR' - the novel storage format proposed in the present study enables a frugal representation of both RNA sequence and structural information in the form of a single string. In spite of having a relatively smaller storage footprint, the resultant 'fastr' string(s) retain all sequence as well as secondary structural information that could be stored using a dot-bracket notation. An implementation of the 'FASTR' methodology is available for download at http://metagenomics.atc.tcs.com/compression/fastr.

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“…Three types of graph drawing approaches can be identified in existing RNA visualization tools [5]: linked graph, circular graph, and classical structure. Although linked graphs and circular graphs support visualization of base pairing, secondary structure motifs can be identified in these types of graphs only with great difficulty.…”

Section: Introductionmentioning

confidence: 99%

“…Therefore, classical structure uses to be the technique of choice when visual inspection of a structure is needed. Multiple solutions have been developed for drawing the classical structure graph of the secondary structure including RNAplot from the ViennaRNA package [6], VARNA [7], RnaViz [8], jViz.RNA [5], sir_graph from the mfold package [9], XRna, PseudoViewer [10] [11] [12], or RNAView [13]. However, only few of those tools and algorithms enable to draw large structures such as large rRNA subunits (RNAplot, RnaViz and RNAView) and only few of them provide non-interactive mode (VARNA and RNAplot)…”

Section: Introductionmentioning

confidence: 99%

RNA Secondary Structure Visualization using Tree Edit Distance

Eliáš¹,

Hoksza²

2016

IJBBB

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RNA secondary structures, both experimental and predicted, are becoming increasingly available which is reflected in the increased demand for tools enabling their analysis. The common first step in the analysis of RNA molecules is visual inspection of their secondary structure. In order to correctly lay out an RNA structure, the notion of optimal layout is required. However, optimal layout of an RNA structure has never been formalized and is largely habitual. To tackle this problem we propose an algorithm capable of visualizing an RNA structure using a related structure with a well-defined layout. The algorithm first converts both structures into tree representations and then uses tree-edit distance algorithm to find out the minimum number of tree edit operations to convert one structure into the other. We couple each tree edit operation with a layout modification operation which is then used to gradually transform the known layout into the target one. The tree edit distance algorithm causes that the common motives are retained and only regions which differ in both the structures are changed in the resulting layout. Visual inspection and planarity evaluation reveals that the algorithm is able to give good layouts even for relatively distant structures while keeping the layout planar. The new method is well suited for situations when one needs to visualize a structure for which a homologous structure with a good visualization is already available.

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jViz.Rna —A Java Tool for RNA Secondary Structure Visualization

Cited by 49 publications

References 11 publications

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes

FASTR: A novel data format for concomitant representation of RNA sequence and secondary structure information

RNA Secondary Structure Visualization using Tree Edit Distance

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