RAG: An update to the RNA-As-Graphs resource

Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

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 benefits of relational database, and improvements to several of the utilities such as directed/labeled graphs and a subgraph search program.Conclusions: The 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.

Original languageEnglish (US)
Article number219
JournalBMC Bioinformatics
Volume12
DOIs
StatePublished - May 31 2011

Fingerprint

RNA
Update
Resources
Graph in graph theory
Clustering Algorithm
Nucleotide Motifs
Cluster Analysis
Clustering
Web Graph
Topology
Dual Graph
RNA Secondary Structure
Secondary Structure
Relational Database
Subgraph
Availability
Clustering algorithms
Databases
Directed graphs

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics
  • Structural Biology

Cite this

RAG : An update to the RNA-As-Graphs resource. / Izzo, Joseph A.; Kim, Namhee; Elmetwaly, Shereef; Schlick, Tamar.

In: BMC Bioinformatics, Vol. 12, 219, 31.05.2011.

Research output: Contribution to journalArticle

Izzo, Joseph A. ; Kim, Namhee ; Elmetwaly, Shereef ; Schlick, Tamar. / RAG : An update to the RNA-As-Graphs resource. In: BMC Bioinformatics. 2011 ; Vol. 12.
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