RAG: RNA-As-Graphs Web Resource

Motivation: The growing RNA genomics and functional studies have led to a significant increase in the repertoire of functional RNAs. Although various RNA structures and motifs are known, as archived in specialized RNA databases, there are no comprehensive, quantitative procedures for cataloguing RNA's structural repertoire. To advance the emerging field of RNA genomics, there is an urgent need to systematically organize existing RNA motifs and to identify novel RNA structures.

Results: We present an RNA motif database, termed RAG for RNA-As-Graphs, based on a graph theory classification that catalogues and ranks all theoretically possible, both existing and candidate, RNA secondary motifs. Essentially, we represent RNA secondary structures as two-dimensional graphs: RNA tree motifs as "tree graphs" and any RNA motifs (including pseudoknots) as "dual graphs". The RNA motifs are catalogued according to their graph vertex number (equivalently, RNA sequence length) and ranked by topological complexity. Our RAG database provides intuitive cataloguing and easy retrieval of all possible RNA secondary motifs. RAG is further exploited to identify structural and functional properties of user-supplied RNA sequences, assisted by links to other structural/functional databases.

Availability: The database is accessible on the web at http://monod.biomath.nyu.edu/rna

Contact: RAG@biomath.nyu.edu.

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