RAG: RNA-As-Graphs web resource

Daniela Fera, Namhee Kim, Nahum Shiffeldrim, Julie Zorn, Uri Laserson, Hin Hark Gan, Tamar Schlick

Research output: Contribution to journalArticle

Abstract

Background: The proliferation of structural and functional studies of RNA has revealed an increasing range of RNA's structural repertoire. Toward the objective of systematic cataloguing of RNA's structural repertoire, we have recently described the basis of a graphical approach for organizing RNA secondary structures, including existing and hypothetical motifs. Description: We now present an RNA motif database based on graph theory, termed RAG for RNA-As-Graphs, to catalogue and rank all theoretically possible, including existing, candidate and hypothetical, RNA secondary motifs. The candidate motifs are predicted using a clustering algorithm that classifies RNA graphs into RNA-like and non-RNA groups. All RNA motifs are filed according to their graph vertex number (RNA length) and ranked by topological complexity. Conclusions: RAG's quantitative cataloguing allows facile retrieval of all classes of RNA secondary motifs, assists identification of structural and functional properties of user-supplied RNA sequences, and helps stimulate the search for novel RNAs based on predicted candidate motifs.

Original languageEnglish (US)
Article number88
JournalBMC Bioinformatics
Volume5
DOIs
StatePublished - Jul 6 2004

Fingerprint

Web Graph
RNA
Resources
Nucleotide Motifs
Graph in graph theory
Topological Complexity
RNA Secondary Structure
Proliferation
Cataloging
Graph theory
Clustering Algorithm
Retrieval
Classify
Vertex of a graph
Range of data
Nucleic Acid Databases
Cluster Analysis
Clustering algorithms

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

Cite this

Fera, D., Kim, N., Shiffeldrim, N., Zorn, J., Laserson, U., Gan, H. H., & Schlick, T. (2004). RAG: RNA-As-Graphs web resource. BMC Bioinformatics, 5, [88]. https://doi.org/10.1186/1471-2105-5-88

RAG : RNA-As-Graphs web resource. / Fera, Daniela; Kim, Namhee; Shiffeldrim, Nahum; Zorn, Julie; Laserson, Uri; Gan, Hin Hark; Schlick, Tamar.

In: BMC Bioinformatics, Vol. 5, 88, 06.07.2004.

Research output: Contribution to journalArticle

Fera, D, Kim, N, Shiffeldrim, N, Zorn, J, Laserson, U, Gan, HH & Schlick, T 2004, 'RAG: RNA-As-Graphs web resource', BMC Bioinformatics, vol. 5, 88. https://doi.org/10.1186/1471-2105-5-88
Fera D, Kim N, Shiffeldrim N, Zorn J, Laserson U, Gan HH et al. RAG: RNA-As-Graphs web resource. BMC Bioinformatics. 2004 Jul 6;5. 88. https://doi.org/10.1186/1471-2105-5-88
Fera, Daniela ; Kim, Namhee ; Shiffeldrim, Nahum ; Zorn, Julie ; Laserson, Uri ; Gan, Hin Hark ; Schlick, Tamar. / RAG : RNA-As-Graphs web resource. In: BMC Bioinformatics. 2004 ; Vol. 5.
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