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e-RNA: a collection of web servers for comparative RNA structure prediction and visualisation
Daniel Lai1, Irmtraud M Meyer2
1Centre for High-Throughput Biology, Department of Computer Science and Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z4, Canada.
Nucleic Acids Research
|May 10, 2014
Summary
e-RNA provides five specialized RNA sequence analysis tools for conserved helices, secondary structures, and pseudo-knots. This free resource aids researchers in complex RNA structure and alignment studies.
Area of Science:
- Bioinformatics
- Computational Biology
- Molecular Biology
Background:
- RNA sequence analysis tools are crucial for understanding RNA structure and function.
- Existing tools may not address specific challenges like pseudo-knots or co-transcriptional folding.
- A comprehensive and accessible resource is needed for advanced RNA analysis.
Purpose of the Study:
- To introduce e-RNA, a free, open-access collection of five novel RNA sequence analysis tools.
- To provide solutions for detecting conserved helices, RNA secondary structures, and pseudo-knots.
- To enhance RNA structure prediction and visualization capabilities.
Main Methods:
- Transat: Detects conserved helices in multiple sequence alignments, including transient and pseudo-knotted structures.
- RNA-Decoder: Employs evolutionary models to find conserved RNA secondary structures in alignments, even with protein-coding regions.
- SimulFold: Co-estimates conserved structure, alignment, and phylogenetic trees for homologous sequences, handling pseudo-knots.
- CoFold: Predicts minimum-free energy structures considering co-transcriptional folding for improved accuracy in long sequences.
- R-chie: Visualizes RNA secondary structures as arc diagrams for comparative analysis of conserved base-pairs.
Main Results:
- The e-RNA platform integrates five distinct tools addressing specific RNA analysis challenges.
- Tools offer advanced capabilities for detecting complex RNA structures like pseudo-knots and transient helices.
- CoFold improves prediction accuracy for long RNA sequences by incorporating co-transcriptional folding.
- R-chie facilitates detailed analysis and comparison of RNA secondary structures.
- The e-RNA server supports parallel job processing and provides results via email or link.
Conclusions:
- e-RNA offers a valuable, integrated suite of specialized tools for advanced RNA sequence analysis.
- The platform empowers researchers to tackle complex problems in RNA structure, evolution, and function.
- e-RNA enhances the accessibility and efficiency of sophisticated RNA bioinformatics analyses.
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