Abstract
BackgroundIn 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures.DescriptionOur RAG update includes a new supervised clustering algorithm that can suggest RNA motifs that may be "RNA-like". We use this utility to describe RNA motifs as three classes: existing, RNA-like, and non-RNA-like. This produces 126 tree and 16,658 dual graphs as candidate RNA-like topologies using the supervised clustering algorithm with existing RNAs serving as the training data. A comparison of this clustering approach to an earlier method shows considerable improvements. Additional RAG features include greatly expanded search capabilities, an interface to better utilize the benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program.ConclusionsThe RAG updates presented here augment the database's intended function - stimulating the search for novel RNA functionality - by classifying available motifs, suggesting new motifs for design, and allowing for more specific searches for specific topologies. The updated RAG web resource offers users a graph-based tool for exploring available RNA motifs and suggesting new RNAs for design.
Highlights
In 2004, we presented a web resource for stimulating the search for novel RNAs, RNA-As-Graphs (RAG), which classified, catalogued, and predicted RNA secondary structure motifs using clustering and build-up approaches
Our RAG update introduces three significant improvements to the RNA Matrix program: first, we have automated the classification of dual graph as well as tree graph topologies; second, we have extended the limit of 200 nt to 1000 nt and of 10 vertices to any number for tree graphs; third, we added a function to specify the direction for the graphs (5’ to 3’) and list common subgraphs between two RNA secondary structures
In the RAG resource, we show a list of synthetic RNA structures determined by experimental methods (X-ray crystal structures or NMR), as listed in NDB, PDB or Pseudobase++
Summary
An improved and updated RAG database has been designed to allow experimentalists and theoreticians to explore currently existing motifs and help suggest novel RNA motifs. The number of available structures has increased, the searching capabilities have been improved, and the web server has a more user-friendly interface and dynamic content. Because of the translation to a combined PHP and MYSQL interface, future updates of RAG will be accessible via the web resource in real time; each tree and dual graph topology has its own sub-page on the web resource that accesses the database and displays all structures corresponding to that particular topology. Each addition to RAG will be displayed instantaneously on its respective online topology page. Availability and Requirements The RAG database, documentation, and software can be accessed on our web server http://www.biomath.nyu. This additional file include the list of Rfam ID whose comparative structure is confirmed by mutagenesis or structure probing (Table S1), correction of the 2004 existing data (Table S2), cross-validation results for tree graphs (Table S3), and tree graphs classified by partial sets (Table S4)
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