ArticleNucleic acids research2015
Web-Beagle: a web server for the alignment of RNA secondary structures.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 38 citations in OpenAlex.
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Tracing the Origin and Evolution of the Secondary Structure of RNA.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A retrospective study on the prevalence and genetic characteristics of porcine parvovirus 6 in Guangxi, China.Frontiers in microbiology · 2026Article
- Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning.Molecules (Basel, Switzerland) · 2025Article
- bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity.Bioinformatics (Oxford, England) · 2025Article
- Human lncRNAs harbor conserved modules embedded in different sequence contexts.Non-coding RNA research · 2024Article
- Exosomal long non-coding RNA-LINC00839 promotes lung adenocarcinoma progression by activating NF-κB signaling pathway.Annals of medicine · 2024Article
- A new tandem repeat-enriched lncRNA XLOC_008672 promotes gastric carcinogenesis by regulating G3BP1 expression.Cancer science · 2024Article
- Integrating cryo-OrbiSIMS with computational modelling and metadynamics simulations enhances RNA structure prediction at atomic resolution.Nature communications · 2024Article
- Dissection of protein and RNA regions required for SPEN binding to XIST A-repeat RNA.RNA (New York, N.Y.) · 2024Article
- bpRNA-align: improved RNA secondary structure global alignment for comparing and clustering RNA structures.RNA (New York, N.Y.) · 2023Article
- RNA localization during early development of the axolotl.Frontiers in cell and developmental biology · 2023Article
- Exploring the landscape of tools and resources for the analysis of long non-coding RNAs.Computational and structural biotechnology journal · 2023Review
- The long non-coding RNA landscape of Candida yeast pathogens.Nature communications · 2021Article
- Translational suppression of SARS-COV-2 ORF8 protein mRNA as a Viable therapeutic target against COVID-19: Computational studies on potential roles of isolated compounds from Clerodendrum volubile leaves.Computers in biology and medicine · 2021Article
- Relative Information Gain: Shannon entropy-based measure of the relative structural conservation in RNA alignments.NAR genomics and bioinformatics · 2021Article
- Assembling mitogenome of Himalayan Black Bear (U. t. laniger) from low depth reads and its application in drawing phylogenetic inferences.Scientific reports · 2021Article
- Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units.Computational and structural biotechnology journal · 2021Article
- Article
- PRIME-3D2D is a 3D2D model to predict binding sites of protein-RNA interaction.Communications biology · 2020Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Web-Beagle (http://beagle.bio.uniroma2.it) is a web server for the pairwise global or local alignment of RNA secondary structures. The server exploits a new encoding for RNA secondary structure and a substitution matrix of RNA structural elements to perform RNA structural alignments. The web server allows the user to compute up to 10 000 alignments in a single run, taking as input sets of RNA sequences and structures or primary sequences alone. In the latter case, the server computes the secondary structure prediction for the RNAs on-the-fly using RNAfold (free energy minimization). The user can also compare a set of input RNAs to one of five pre-compiled RNA datasets including lncRNAs and 3' UTRs. All types of comparison produce in output the pairwise alignments along with structural similarity and statistical significance measures for each resulting alignment. A graphical color-coded representation of the alignments allows the user to easily identify structural similarities between RNAs. Web-Beagle can be used for finding structurally related regions in two or more RNAs, for the identification of homologous regions or for functional annotation. Benchmark tests show that Web-Beagle has lower computational complexity, running time and better performances than other available methods.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.