Efficient Chaining of Seeds in Ordered Trees
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m 2 log(m)) in time and O(m 2) in space.
KeywordsTime Complexity Maximum Chain Order Tree Valid Mapping Border Node
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