Bioinformatics Advance Access originally published online on February 12, 2004
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Bioinformatics 20(8) © Oxford University Press 2004; all rights reserved.
RAG: RNA-As-Graphs database—concepts, analysis, and features
1 Department of Chemistry, New York University, New York, NY 10003, USA, 2 Howard Hughes Medical Institute, 100, Washington Square East and 3 Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
Received on May 30, 2003; revised on October 27, 2003; accepted on November 11, 2003
Advance Access Publication February 12, 2004
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
Contact: schlick{at}nyu.edu
* To whom correspondence should be addressed.
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