Web-Beagle: a web server for the alignment of RNA secondary structures: Figure 1.

Mattei, Eugenio; Pietrosanto, Marco; Ferré, Fabrizio; Helmer-Citterich, Manuela

doi:10.1093/nar/gkv489

“…To do so, we first predicted the secondary structure of the annotated lncRNAs in the four species using RNAfold software from Vienna package [42]. Since lncRNAs are known to be weakly conserved at the sequence level, we used the software BEAGLE [43] to study the secondary structure similarity of lncRNAs, since this algorithm compares structures without requiring a sequence alignment. We discarded other available structure comparison tools (e.g.…”

Section: Synteny As a Proxy To Identify Homologous Lncrnasmentioning

confidence: 99%

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Pegueroles

¹

,

Iraola-Guzmán

²

,

Chorostecki

³

et al. 2019

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Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four Caenorhabditis species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs. ARTICLE HISTORY

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“…To evaluate the presence of conserved structural elements within lncRNAs we used the software BEAGLE 46 . This software compares secondary structures encoded using the BEAR notation by performing pairwise global or local alignments and provides measures of structural similarity and statistical significance for each alignment.…”

Section: Classification Of Lncrna Into Secondary Structure Based Famimentioning

confidence: 99%

“…Knowing that selection may act on conservation of the secondary structure rather than on sequence, we analyzed the patterns of structural conservation of lncRNAs. Since lncRNAs are known to be weakly conserved at the sequence level, we used the software BEAGLE 46 to study the secondary structure similarity of lncRNAs, since this algorithm compares structures without requiring a sequence alignment. The software provides an associated zscore for each comparison, and a z-score higher than three is indicative of significant similarities.…”

Section: Synteny As a Proxy To Identify Homologous Lncrnasmentioning

confidence: 99%

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Pegueroles

¹

,

Iraola-Guzmán

²

,

Chorostecki

³

et al. 2018

Preprint

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Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in numerous organisms, but our knowledge of lncRNAs in non vertebrate species remains very limited. Here, we annotated lncRNAs using transcriptomic data from the same larval stage of four Caenorhabditis species. The number of annotated lncRNAs in self-fertile nematodes was lower than in out-crossing species. We used a combination of approaches to identify putatively homologous lncRNAs: synteny, sequence conservation, and structural conservation. We classified a total of 1,532 out of 7,635 genes from the four species into families of lncRNAs with conserved synteny and expression at the larval stage, suggesting that a large fraction of the predicted lncRNAs may be species specific. Despite both sequence and local secondary structure seem to be poorly conserved, sequences within families frequently shared BLASTn hits and short sequence motifs, which were more likely to be unpaired in the predicted structures. We provide the first multi-species catalog of lncRNAs in nematodes and identify groups of lncRNAs with conserved synteny and expression, that share exposed motifs.

show abstract

“…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%

“…In [32], a new context-aware encoding representation for RNA secondary structure named as BEAR is designed and an RNA structural alignment based on BEAR encoding is proposed by integrating a constructed substitution matrix of RNA structural elements with Needleman-Wunsch algorithm. The web server Web-Beagle [29] of RNA structural alignment based on BEAR encoding is developed. Among the above alignment-based tools, RNAdistance and RNApdist are the two most widely-used tools, which have been included in the Vienna RNA package [31].…”

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

Li

¹

,

Shi

²

,

Xie

³

et al. 2017

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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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Web-Beagle: a web server for the alignment of RNA secondary structures: Figure 1.

Cited by 33 publications

References 24 publications

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

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

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