RAG: An Update to the RNA-As-Graphs Resource

Background: 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. With the increased availability of secondary structures in recent years, we update the RAG resource and provide various improvements for analyzing RNA structures. Description: Our 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 benefi...

• Type: Journal
• Year: 2011
• Where: BMCBI
• Authors: Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tamar Schlick
• Keywords: Biometrics, BMCBI 2011, Clustering Algorithm, RNA Motifs, RNA Structures