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

Subtree Homeomorphism Score
� Let T 1 and T 2 be two ordered, rooted, homeomorphic trees.
� A mapping µ : T 1 → T 2 is a one-to-one map from the nodes of T 1 to the nodes of T 2
that preserves the ancestor relations of the nodes and their relative order.
� The subtree homeomorphism score of the mapping, denoted S(µ), is
a user defined nodeto-node
similarity
score function
edge-to-edge similarity
score function where e u�T1,
e v�T2 are corresponding
edges.
The penalty of
deleting a
degree-2-node
from T 2
The penalty for
deleting any
other node.