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e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation

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Item Type:Article
Title:e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation
Creators Name:Lai, D. and Meyer, I.M.
Abstract:e-RNA offers a free and open-access collection of five published RNA sequence analysis tools, each solving specific problems not readily addressed by other available tools. Given multiple sequence alignments, Transat detects all conserved helices, including those expected in a final structure, but also transient, alternative and pseudo-knotted helices. RNA-Decoder uses unique evolutionary models to detect conserved RNA secondary structure in alignments which may be partly protein-coding. SimulFold simultaneously co-estimates the potentially pseudo-knotted conserved structure, alignment and phylogenetic tree for a set of homologous input sequences. CoFold predicts the minimum-free energy structure for an input sequence while taking the effects of co-transcriptional folding into account, thereby greatly improving the prediction accuracy for long sequences. R-chie is a program to visualise RNA secondary structures as arc diagrams, allowing for easy comparison and analysis of conserved base-pairs and quantitative features. The web site server dispatches user jobs to a cluster, where up to 100 jobs can be processed in parallel. Upon job completion, users can retrieve their results via a bookmarked or emailed link. e-RNA is located at http://www.e-rna.org.
Keywords:Algorithms, Computer Graphics, Internet, Nucleic Acid Conformation, RNA, RNA Sequence Analysis, Sequence Alignment, Software
Source:Nucleic Acids Research
Publisher:Oxford University Press
Number:Web Server issue
Page Range:W373-W376
Date:1 July 2014
Official Publication:https://doi.org/10.1093/nar/gku292
PubMed:View item in PubMed

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