In the last few years, we have  seen a rapid increase of the number of
known non-protein  coding ribonucleic acids (ncRNAs).   It is becoming
clear  that RNAs  are also  playing an  important in  cell regulation.
However, for a significant fraction  of them, the mechanisms of action
remain  unclear.   Their  signature  combines structure  and  sequence
information.   In most  cases,  they are  difficult  to identify  from
sequence alone.  Traditional approaches to identify RNA motifs seek to
find  a conserved motif  with minimum  free energy  in an  ensemble of
aligned  sequences.   Our  group  is  developing  new  approaches  for
discovering consensus secondary structure motifs in a set of unaligned
RNA  sequences.  State-of-the-art  data  structures, including  suffix
arrays, are  used to efficiently search  the space of  RNA motifs.  We
have  recently developed  two software  systems, X-Dynalign  and Seed,
that can be used to  assist the identification and characterisation of
new motifs.   Determining RNA secondary structure  motifs is important
for     understanding     the     structure-function     relationship,
post-transcriptional regulation, as well as identifying RNA targets.