RNAMotifScanX: a graph alignment approach for RNA structural motif identification

Zhong, Cuncong; Zhang, Shaojie

doi:10.1261/rna.044891.114

Cited by 25 publications

(23 citation statements)

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“…2) is specified. In addition, RNAMotifScanX ( 48 ), which is also designed by our lab for searching RNA 3D structural motifs in the single-stranded regions, can be applied since those RNAs are relatively short and are dominated by loops. STAR3D was compared with ARTS, SARA and LaJolla one by one.…”

Section: Resultsmentioning

confidence: 99%

STAR3D: a stack-based RNA 3D structural alignment tool

Zhang

2015

Nucleic Acids Res

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The various roles of versatile non-coding RNAs typically require the attainment of complex high-order structures. Therefore, comparing the 3D structures of RNA molecules can yield in-depth understanding of their functional conservation and evolutionary history. Recently, many powerful tools have been developed to align RNA 3D structures. Although some methods rely on both backbone conformations and base pairing interactions, none of them consider the entire hierarchical formation of the RNA secondary structure. One of the major issues is that directly applying the algorithms of matching 2D structures to the 3D coordinates is particularly time-consuming. In this article, we propose a novel RNA 3D structural alignment tool, STAR3D, to take into full account the 2D relations between stacks without the complicated comparison of secondary structures. First, the 3D conserved stacks in the inputs are identified and then combined into a tree-like consensus. Afterward, the loop regions are compared one-to-one in accordance with their relative positions in the consensus tree. The experimental results show that the prediction of STAR3D is more accurate for both non-homologous and homologous RNAs than other state-of-the-art tools with shorter running time.

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Section: Resultsmentioning

confidence: 99%

STAR3D: a stack-based RNA 3D structural alignment tool

Zhang

2015

Nucleic Acids Res

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“…Furthermore, different motifs may be classified together if they share common patterns in their secondary structures. 8 The 3D structures of the remaining loops in refined clusters were manually checked to categorize them into sub-clusters. After that, the secondary and tertiary structural features of sub-clusters were extracted for function annotation, and the identical sub-clusters were investigated through comparing these features.…”

Section: Motif Family Identificationmentioning

confidence: 99%

“…All these three pairing interactions are in the secondary structural consensus of sarcin-ricins. 8 However, in common sarcin-ricins, the cis H/W base pair U429/A431 should be a cis H/S interaction between U429/A430. The possible reason for this difference is that the strand U427→C433 is longer than it in the consensus.…”

Section: Sarcin-ricinmentioning

confidence: 99%

“…6 Based on this idea, RNAMotifScan is proposed to search new motif candidates that share non-canonical base-base interaction patterns with the query. 7,8 The benchmarking results show that RNAMotifScan outperforms other state-of-the-art RNA structural motif searching tools, especially for the instances with geometric variations caused by insertions or deletions.…”

Section: Introductionmentioning

confidence: 99%

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De novo discovery of structural motifs in RNA 3D structures through clustering

Islam

Zhong

et al. 2017

Preprint

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As functional components in three-dimensional conformation of an RNA, the RNA structural motifs provide an easy way to associate the molecular architectures with their biological mechanisms. In the past years, many computational tools have been developed to search motif instances by using the existing knowledge of well-studied families. Recently, with the rapidly increasing number of resolved RNA 3D structures, there is an urgent need to discover novel motifs with the newly presented information. In this work, we classify all the loops in non-redundant RNA 3D structures to detect plausible RNA structural motif families by using a clustering pipeline. Compared with other clustering approaches, our method has two benefits: first, the underlying alignment algorithm is tolerant to the variations in 3D structures; second, sophisticated downstream analysis has been performed to ensure the clusters are valid and easily applied to further research. The final clustering results contain many interesting new variants of known motif families, such as GNAA tetraloop, kink-turn, sarcin-ricin, and T-loop. We have also discovered potential novel functional motifs conserved in ribosomal RNA, sgRNA, SRP RNA, riboswitch, and ribozyme.

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“…Studies of the RNA 3D structures can provide essential insights into their functionalities. With the increasing number of RNA structures deposited in Protein Data Bank (PDB) ( 5 ), analyzing their 3D structures, particularly the interactions between nucleotides, are attracting increasing research focus ( 6 – 8 ).…”

Section: Introductionmentioning

confidence: 99%

CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures

Islam

Zhang

2017

Nucleic Acids Research

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The analysis of RNA tertiary structure is hindered by the fact that not too many structural data are available and a significant amount of them are in low resolution. Due to the atomic coordinate errors posed by the limitations of low-resolution RNA three-dimensional structures, it becomes a critical challenge to extract key geometric characteristics of RNA, particularly, the interaction of bases. To address this issue, we have devised a comparative method, named CompAnnotate, that utilizes more precise structural information of high-resolution homologs to annotate the base-pairing interactions in the low-resolution structures, by aligning and making comparative geometric assessments. The benchmarking results show that our method can improve the annotations of the existing methods significantly. We have achieved different levels of improvements for various methods and datasets, including an example of significant sensitivity and precision enhancement from 28 to 57% and from 53 to 82%, respectively.

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RNAMotifScanX: a graph alignment approach for RNA structural motif identification

Cited by 25 publications

References 50 publications

STAR3D: a stack-based RNA 3D structural alignment tool

STAR3D: a stack-based RNA 3D structural alignment tool

De novo discovery of structural motifs in RNA 3D structures through clustering

CompAnnotate: a comparative approach to annotate base-pairing interactions in RNA 3D structures

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