RDM Circles A program to automate the comparative analysis of RNA secondary structure
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RDM Circles Tags

analysis structure RNA Batch RNA secondary installs secondary comparative RNA world RNA to Aminoacid RNA polymerase RNA structure Comparative analysis phylogenetic analysis structure analysis view RNA secondary structure RNA secondary structure viewer RNA structure visualization automate analysis procedure RNA-seq data analysis decode RNA structure secondary program RNA secondary structure comparative map viewer RNA sequence analysis draw secondary RNA structure create RNA structure RNA structure generator secondary structure prediction comparative genomics viewer visualize comparative genomics RNA secondary structures RNA analysis analyze comparative data comparative data analysis brain structure analysis RNA Alignment periodic structure analysis data structure analysis RNA Ontology Consortium RNA backbone nomenclature secondary education comparative diagrams

RDM Circles Description

The RDM Circles application was designed to be an experimental Windows program for inferring RNA secondary structure using the comparative method. Comparative analysis is the preferred method of inferring RNA secondary structure, but its use requires considerable expertise and manual effort. As the importance of secondary structure for accurate sequence alignment and phylogenetic analysis becomes increasingly realised, the need for secondary structure models for diverse taxonomic groups becomes more pressing. Maximum weight matching (MWM) is graph-theoretic approach to inferring RNA secondary structure that shows considerable promise. It takes as input a set of base pairing scores that can be derived from a range of sources, such as free energy considerations, mutual information, or experimental data. These data can be represented as a folding graph where the vertices are alignment positions, and the lines or edges connecting a pair of vertices are given a weight proportional to the amount of evidence for that pairing. A matching is a subgraph of the folding graph in which no vertex is connected to more than one other vertex. The matching with the greatest total edge weight is the taken to be the best estimate of the RNA structure. This matching can include information on both secondary and tertiary structure, such as pseudoknots. MWM can greatly speed up the process of comparative structure analysis of RNA sequences, and has been tested successfully on tRNA, SRP RNA, and 16S rRNA sequences.

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