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

Subtree Homeomorphism Score
� The cost function varies from one application to another,
depending upon the amount of information supplied with the
query.
� The simplest one just compares the topology of the
structures.
� More complex functions include length differences of the
structural elements, sequence conservation and pseudoknot
matching.
� The node deletion score (i.e., gap penalty) reflects the tradeoff
between a gap and a mismatch. As the gap penalty increases,
the algorithm tends to match distant nodes to avoid gaps. As
different values may suit different needs, our tool enables
users to set this parameter for each run.