“A structure based flexible search method for motifs in RNA” Isana ...

Comparison of ordered rooted
trees
� Ordered tree comparison is generally computed by tree edit
distance, which allows various forms of deletions and insertions in
both query and target.
� The search for small non-coding RNAs naturally yields a more
specific tree search formulation since we do not allow deletions in
the query.
� In our method we apply a weighted pattern matching algorithm for
finding the best homeomorphic mapping between two rooted
ordered trees.
� Specific constraints on the searched motif can be defined in the
input to the search: structural constraints (lengths), allowing or
forbidding element deletion in the target, sequence constraints
(existence of sibling pseudoknots, local conserved sequence
segments).