RNAML: A standard syntax for exchanging RNA information

Waugh, Allison; Gendron, Patrick; Altman, Russ B.; Brown, James W.; Case, David A.; Gautheret, Daniel; Harvey, Stephen C.; Leontis, Neocles B.; Westbrook, John D.; Westhof, Éric; Zuker, Michael; Major, François

doi:10.1017/s1355838202028017

Cited by 95 publications

(64 citation statements)

References 14 publications

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“…The number of nucleotides in the three single-stranded junctions (i.e., those not involved in standard helical Watson-Crick pairings) are given in Table 1. A standard helix was considered to exist when there were at least two consecutive canonical Watson-Crick pairs (Waugh et al 2002). Three groups (or families) of three-way junctions could be isolated depending on the lengths of the junction strands (Fig.…”

Section: Methods and Resultsmentioning

confidence: 99%

“…Four of these are implicated in the core of three-way junctions belonging to family C. The L11 rRNA has been described as a four-way helical junction (Wimberly et al 1999). According to the definition of a minimal helix as two stacked Watson-Crick base pairs (Waugh et al 2002), helix 1082 (Escherichia coli numbering) should not be considered as a helix. It is rather a tri-loop closed by a non-Watson-Crick base pair (Lee et al 2003).…”

Section: Family Cmentioning

confidence: 99%

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Topology of three-way junctions in folded RNAs

Lescoute¹,

Westhof²

2005

RNA

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281

308

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The three-way junctions contained in X-ray structures of folded RNAs have been compiled and analyzed. Three-way junctions with two helices approximately coaxially stacked can be divided into three main families depending on the relative lengths of the segments linking the three Watson-Crick helices. Each family has topological characteristics with some conservation in the nonWatson-Crick pairs within the linking segments as well as in the types of contacts between the segments and the helices. The most populated family presents tertiary interactions between two helices as well as extensive shallow/minor groove contacts between a linking segment and the third helix. On the basis of the lengths of the linking segments, some guidelines could be deduced for choosing a topology for a three-way junction on the basis of a secondary structure. Examples and prediction bas'ed on those rules are discussed.

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Section: Methods and Resultsmentioning

confidence: 99%

Section: Family Cmentioning

confidence: 99%

Topology of three-way junctions in folded RNAs

Lescoute¹,

Westhof²

2005

RNA

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281

308

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“…A digital object model (DOM) of the structural annotations was built based on the RNAML (Waugh et al 2002) output of RNAView and used to identify the different structural elements (helices, junctions, hairpin loops, and single-stranded regions) of the structure. The software developed to do this analysis (rnaDB.py) is freely available for download from https://simtk.org/home/rnadb/.…”

Section: Informatics For Rna Structural Analysismentioning

confidence: 99%

Coplanar and coaxial orientations of RNA bases and helices

Laederach¹,

Chan²,

Schwartzman³

et al. 2007

RNA

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Electrostatic interactions, base-pairing, and especially base-stacking dominate RNA three-dimensional structures. In an A-form RNA helix, base-stacking results in nearly perfect parallel orientations of all bases in the helix. Interestingly, when an RNA structure containing multiple helices is visualized at the atomic level, it is often possible to find an orientation such that only the edges of most bases are visible. This suggests that a general aspect of higher level RNA structure is a coplanar arrangement of base-normal vectors. We have analyzed all solved RNA crystal structures to determine the degree to which RNA base-normal vectors are globally coplanar. Using a statistical test based on the Watson-Girdle distribution, we determined that 330 out of 331 known RNA structures show statistically significant (p < 0.05; false discovery rate [FDR] = 0.05) coplanar normal vector orientations. Not surprisingly, 94% of the helices in RNA show bipolar arrangements of their base-normal vectors (p < 0.05). This allows us to compute a mean axis for each helix and compare their orientations within an RNA structure. This analysis revealed that 62% (208/331) of the RNA structures exhibit statistically significant coaxial packing of helices (p < 0.05, FDR = 0.08). Further analysis reveals that the bases in hairpin loops and junctions are also generally planar. This work demonstrates coplanar base orientation and coaxial helix packing as an emergent behavior of RNA structure and may be useful as a structural modeling constraint.

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“…RNAML (Waugh et al 2002) is used to store and export information on putative ncRNA. RNAML is a standard XML syntax for RNA information.…”

Section: Data Storagementioning

confidence: 99%

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

Cros¹,

Monte²,

Mariette³

et al. 2011

RNA

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The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. Most genome sequences released today still come with sets of tRNAs and rRNAs as the only annotated RNA elements, ignoring hundreds of other RNA families. We have developed a web environment that is dedicated to noncoding RNA (ncRNA) prediction, annotation, and analysis and allows users to run a variety of tools in an integrated and flexible manner. This environment offers complementary ncRNA gene finders and a set of tools for the comparison, visualization, editing, and export of ncRNA candidates. Predictions can be filtered according to a large set of characteristics. Based on this environment, we created a public website located at http://RNAspace.org. It accepts genomic sequences up to 5 Mb, which permits for an online annotation of a complete bacterial genome or a small eukaryotic chromosome. The project is hosted as a Source Forge project (http://rnaspace.sourceforge.net/).

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RNAML: A standard syntax for exchanging RNA information

Cited by 95 publications

References 14 publications

Topology of three-way junctions in folded RNAs

Topology of three-way junctions in folded RNAs

Coplanar and coaxial orientations of RNA bases and helices

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

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