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(m2 log(m)) in time and O(m2 ) in space.

• Type: Journal
• Year: 2010
• Where: IWOCA
• Authors: Julien Allali, Cedric Chauve, Pascal Ferraro, Anne-Laure Gaillard
• Keywords: Algorithms, Constant Size Seeds, IWOCA 2010, Non Overlapping Seeds, RNA Secondary Structures