Searching for 2D RNA geometries in bacterial genomes
SCG '04 Proceedings of the twentieth annual symposium on Computational geometry
Contraction Graphs for Representation and Analysis of RNA Secondary Structure
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
Efficiently Mining Frequent Trees in a Forest: Algorithms and Applications
IEEE Transactions on Knowledge and Data Engineering
Graph nodes clustering with the sigmoid commute-time kernel: A comparative study
Data & Knowledge Engineering
Spectral graph partitioning analysis of in vitro synthesized RNA structural folding
PRIB'06 Proceedings of the 2006 international conference on Pattern Recognition in Bioinformatics
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Motivation: Understanding RNA's structural diversity is vital for identifying novel RNA structures and pursuing RNA genomics initiatives. By classifying RNA secondary motifs based on correlations between conserved RNA secondary structures and functional properties, we offer an avenue for predicting novel motifs. Although several RNA databases exist, no comprehensive schemes are available for cataloguing the range and diversity of RNA's structural repertoire. Results: Our RNA-As-Graphs (RAG) database describes and ranks all mathematically possible (including existing and candidate) RNA secondary motifs on the basis of graphical enumeration techniques. We represent RNA secondary structures as two-dimensional graphs (networks), specifying the connectivity between RNA secondary structural elements, such as loops, bulges, stems and junctions. We archive RNA tree motifs as 'tree graphs' and other RNAs, including pseudoknots, as general 'dual graphs'. All RNA motifs are catalogued by graph vertex number (a measure of sequence length) and ranked by topological complexity. The RAG inventory immediately suggests candidates for novel RNA motifs, either naturally occurring or synthetic, and thereby might stimulate the prediction and design of novel RNA motifs. Availability: The database is accessible on the web at http://monod.biomath.nyu.edu/rna