Alignments of RNA Structures

Blin, Guillaume; Denise, Alain; Dulucq, Serge; Herrbach, Claire; Touzet, Hélène

doi:10.1109/tcbb.2008.28

Cited by 49 publications

(64 citation statements)

References 31 publications

(35 reference statements)

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“…We compare six tools: RNAdistance [19], RNAforester [10], MiGaL [8], TreeMatching [12], Gardenia [9], NestedAlign [20], and RNAStrAT [11]. These tools rely on different models of secondary structures, such as ordered trees, multilayers models, arc-annotated sequences, but are all based on the edit distance and alignment approach pioneered in [19, 21–23].…”

Section: Illustration: Comparison Models and The Srp Familymentioning

confidence: 99%

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Allali

Saule

Chauve

et al. 2012

Advances in Bioinformatics

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The pairwise comparison of RNA secondary structures is a fundamental problem, with direct application in mining databases for annotating putative noncoding RNA candidates in newly sequenced genomes. An increasing number of software tools are available for comparing RNA secondary structures, based on different models (such as ordered trees or forests, arc annotated sequences, and multilevel trees) and computational principles (edit distance, alignment). We describe here the website BRASERO that offers tools for evaluating such software tools on real and synthetic datasets.

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Section: Illustration: Comparison Models and The Srp Familymentioning

confidence: 99%

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

Allali

Saule

Chauve

et al. 2012

Advances in Bioinformatics

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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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“…For RNA genes, due to the importance of the structure in terms of biological function, it is natural to consider both the sequence and secondary structure when comparing genes. Most RNA comparison methods can be classified in two families: (i) tools requiring the knowledge of an RNA secondary structure, such as RNAforester [9] or Gardenia [4] to cite only two (see [3] for a thorough evaluation of such methods), and (ii) tools taking only RNA sequences as input and using covariance models or base pairing probabilities such as LocaRNA [20] or Infernal [13]. The first family of approaches relies on the classical notions of edit distance and alignment.…”

Section: Introductionmentioning

confidence: 99%

Chaining Sequence/Structure Seeds for Computing RNA Similarity

Bourgeade

Chauve

Allali

2015

Journal of Computational Biology

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Abstract. We describe a new method to compare a query RNA with a static set of target RNAs. Our method is based on (i) a static indexing of the sequence/structure seeds of the target RNAs, (ii) searching the target RNAs by detecting seeds of the query present in the target, chaining these seeds in promising candidate homologs, then (iii) completing the alignment using an anchor-based exact alignment algorithm. We apply our method on the benchmark Bralibase2.1 and compare its accuracy and efficiency with the exact method LocaRNA and its recent seeds-based speed-up ExpLoc-P. Our pipeline RNA-unchained greatly improves computation time of LocaRNA and is comparable to the one of ExpLoc-P, while improving the overall accuracy of the final alignments.

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Alignments of RNA Structures

Cited by 49 publications

References 31 publications

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

BRASERO: A Resource for Benchmarking RNA Secondary Structure Comparison Algorithms

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

Chaining Sequence/Structure Seeds for Computing RNA Similarity

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