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.
Click to go back to the publication list