Efficient alignment of RNA secondary structures using sparse dynamic programming

Zhong, Cuncong; Zhang, Shaojie

doi:10.1186/1471-2105-14-269

Cited by 9 publications

(5 citation statements)

References 41 publications

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“…Non-Sankoff algorithms separate these two processes: folding and alignments. The main methods include CMfinder [22], LARA [23], RNAdistance [4], RNAStrAt [24], RNAforester [25], SCARNA [26], gardenia [27], ERA [28] Web-Beagle [29] and RNApdist [30]. RNAdistance, RNAforester, RNApdist and RNAStrAt are all tree-based approaches.…”

Section: Introductionmentioning

confidence: 99%

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

Shi

Xie

et al. 2017

BMC Bioinformatics

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BackgroundRNAs have been found to carry diverse functionalities in nature. Inferring the similarity between two given RNAs is a fundamental step to understand and interpret their functional relationship. The majority of functional RNAs show conserved secondary structures, rather than sequence conservation. Those algorithms relying on sequence-based features usually have limitations in their prediction performance. Hence, integrating RNA structure features is very critical for RNA analysis. Existing algorithms mainly fall into two categories: alignment-based and alignment-free. The alignment-free algorithms of RNA comparison usually have lower time complexity than alignment-based algorithms.ResultsAn alignment-free RNA comparison algorithm was proposed, in which novel numerical representations RNA-TVcurve (triple vector curve representation) of RNA sequence and corresponding secondary structure features are provided. Then a multi-scale similarity score of two given RNAs was designed based on wavelet decomposition of their numerical representation. In support of RNA mutation and phylogenetic analysis, a web server (RNA-TVcurve) was designed based on this alignment-free RNA comparison algorithm. It provides three functional modules: 1) visualization of numerical representation of RNA secondary structure; 2) detection of single-point mutation based on secondary structure; and 3) comparison of pairwise and multiple RNA secondary structures. The inputs of the web server require RNA primary sequences, while corresponding secondary structures are optional. For the primary sequences alone, the web server can compute the secondary structures using free energy minimization algorithm in terms of RNAfold tool from Vienna RNA package.ConclusionRNA-TVcurve is the first integrated web server, based on an alignment-free method, to deliver a suite of RNA analysis functions, including visualization, mutation analysis and multiple RNAs structure comparison. The comparison results with two popular RNA comparison tools, RNApdist and RNAdistance, showcased that RNA-TVcurve can efficiently capture subtle relationships among RNAs for mutation detection and non-coding RNA classification. All the relevant results were shown in an intuitive graphical manner, and can be freely downloaded from this server. RNA-TVcurve, along with test examples and detailed documents, are available at: http://ml.jlu.edu.cn/tvcurve/.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-017-1481-7) contains supplementary material, which is available to authorized users.

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Section: Introductionmentioning

confidence: 99%

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

Shi

Xie

et al. 2017

BMC Bioinformatics

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“…The issue is the difficulty of integrating the conventional RNA secondary structure alignment algorithms into the RNA 3D structural comparison. Given the high time complexity of these algorithms [at least O ( n 3 )] ( 24 – 27 ), applying them directly to the relatively complicated atomic coordinates will increase the computational complexity significantly.…”

Section: Introductionmentioning

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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“…Among others, one can point out applications for comparative analysis (e.g. Vienna RNA Package ( 1 )), secondary structure alignment (Dynalig ( 2 ), ERA ( 3 )), visualisation (see PseudoViewer ( 4 ), VARNA ( 5 ), RNAMovies ( 6 )), identification of RNA 3D fragments with a user-defined secondary structure topology (RNA FRABASE ( 7 , 8 ), FASTR3D ( 9 )) or automated RNA 3D structure prediction (RNA2D3D ( 10 ), MC-Sym ( 11 ), RNAComposer ( 12 )).…”

Section: Introductionmentioning

confidence: 99%

RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

Antczak¹,

Żok²,

Popenda³

et al. 2014

Nucleic Acids Research

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In RNA structural biology and bioinformatics an access to correct RNA secondary structure and its proper representation is of crucial importance. This is true especially in the field of secondary and 3D RNA structure prediction. Here, we introduce RNApdbee—a new tool that allows to extract RNA secondary structure from the pdb file, and presents it in both textual and graphical form. RNApdbee supports processing of knotted and unknotted structures of large RNAs, also within protein complexes. The method works not only for first but also for high order pseudoknots, and gives an information about canonical and non-canonical base pairs. A combination of these features is unique among existing applications for RNA structure analysis. Additionally, a function of converting between the text notations, i.e. BPSEQ, CT and extended dot-bracket, is provided. In order to facilitate a more comprehensive study, the webserver integrates the functionality of RNAView, MC-Annotate and 3DNA/DSSR, being the most common tools used for automated identification and classification of RNA base pairs. RNApdbee is implemented as a publicly available webserver with an intuitive interface and can be freely accessed at http://rnapdbee.cs.put.poznan.pl/.

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Efficient alignment of RNA secondary structures using sparse dynamic programming

Cited by 9 publications

References 41 publications

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

RNA-TVcurve: a Web server for RNA secondary structure comparison based on a multi-scale similarity of its triple vector curve representation

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

RNApdbee—a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs

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