DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities

Ferré, Fabrizio; Ponty, Yann; Lorenz, William Andrew; Clote, Peter

doi:10.1093/nar/gkm334

Cited by 57 publications

(65 citation statements)

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“…Additional methods locate small predefined motifs in larger structures and, as such, are useful for finding new occurrences of known motifs (Duarte et al 2003;Harrison et al 2003;Sarver et al 2007). The more complicated problem of finding a priori unknown common substructures is partially addressed by COMPADRES (Wadley and Pyle 2004), DIAL (Ferrè et al 2007), and the method described by Hershkovitz et al (2003). The three methods can detect spatially conserved fragments of successive nucleotides.…”

Section: Introductionmentioning

confidence: 99%

Analysis and classification of RNA tertiary structures

Abraham¹,

Dror²,

Nussinov³

et al. 2008

RNA

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There is a fast growing interest in noncoding RNA transcripts. These transcripts are not translated into proteins, but play essential roles in many cellular and pathological processes. Recent efforts toward comprehension of their function has led to a substantial increase in both the number and the size of solved RNA structures. With the aim of addressing questions relating to RNA structural diversity, we examined RNA conservation at three structural levels: primary, secondary, and tertiary structure. Additionally, we developed an automated method for classifying RNA structures based on spatial (three-dimensional [3D]) similarity. Applying the method to all solved RNA structures resulted in a classified database of RNA tertiary structures (DARTS). DARTS embodies 1333 solved RNA structures classified into 94 clusters. The classification is hierarchical, reflecting the structural relationship between and within clusters. We also developed an application for searching DARTS with a new structure. The search is fast and its performance was successfully tested on all solved RNA structures since the creation of DARTS. A user-friendly interface for both the database and the search application is available online. We show intracluster and intercluster similarities in DARTS and demonstrate the usefulness of the search application. The analysis reveals the current structural repertoire of RNA and exposes common global folds and local tertiary motifs. Further study of these conserved substructures may suggest possible RNA domains and building blocks. This should be beneficial for structure prediction and for gaining insights into structure-function relationships.

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Section: Introductionmentioning

confidence: 99%

Analysis and classification of RNA tertiary structures

Abraham¹,

Dror²,

Nussinov³

et al. 2008

RNA

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show abstract

“…Examples of the 3D geometry-based tools include NASSAM (Harrison et al 2003), PRIMOS (Duarte et al 2003), ARTS (Dror et al 2005), DIAL (Ferrè et al 2007), FR3D (Sarver et al 2008), and the shape histogram method (Apostolico et al 2009) etc. Other tools try to find conserved base-interaction patterns between the query and motif, such as MC-Search (Hoffmann et al 2003), FR3D symbolic search (Sarver et al 2008), and RNAMotifScan (Zhong et al 2010) etc.…”

Section: Introductionmentioning

confidence: 99%

RNAMotifScanX: a graph alignment approach for RNA structural motif identification

Zhong

Zhang

2015

RNA

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RNA structural motifs are recurrent three-dimensional (3D) components found in the RNA architecture. These RNA structural motifs play important structural or functional roles and usually exhibit highly conserved 3D geometries and base-interaction patterns. Analysis of the RNA 3D structures and elucidation of their molecular functions heavily rely on efficient and accurate identification of these motifs. However, efficient RNA structural motif search tools are lacking due to the high complexity of these motifs. In this work, we present RNAMotifScanX, a motif search tool based on a base-interaction graph alignment algorithm. This novel algorithm enables automatic identification of both partially and fully matched motif instances. RNAMotifScanX considers noncanonical base-pairing interactions, base-stacking interactions, and sequence conservation of the motifs, which leads to significantly improved sensitivity and specificity as compared with other state-of-the-art search tools. RNAMotifScanX also adopts a carefully designed branch-and-bound technique, which enables ultra-fast search of large kink-turn motifs against a 23S rRNA. The software package RNAMotifScanX is implemented using GNU C++, and is freely available from http://genome.ucf.edu/RNAMotifScanX.

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“…LaJolla uses an n-gram model to analyze sequences derived from nucleotide torsion angles (4). Similarly, PRIMOS/AMIGOS (5) and DIAL (6) also represent nucleotides with torsion angles and align the sequences encoded by the torsion angle representation. These methods do not necessarily produce globally similar alignment between two RNA structures (i.e.…”

Section: Introductionmentioning

confidence: 99%

RASS: a web server for RNA alignment in the joint sequence-structure space

He¹,

Steppi²,

Laborde³

et al. 2014

Nucleic Acids Research

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Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relationships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) information. Sequences and 3D structures contain non-overlapping sets of information that both determine RNA functions. When comparing RNA 3D structures, both types of information need to be taken into account. However, few methods compare RNA structures using both sequence and 3D structure information. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to research community. The web server is located at http://cloud.stat.fsu.edu/RASS/.

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DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities

Cited by 57 publications

References 50 publications

Analysis and classification of RNA tertiary structures

Analysis and classification of RNA tertiary structures

RNAMotifScanX: a graph alignment approach for RNA structural motif identification

RASS: a web server for RNA alignment in the joint sequence-structure space

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