Efficient chaining of seeds in ordered trees
Conference object, Article, Preprint
- Publisher: Elsevier BV
Journal of Discrete Algorithms,
Theoretical Computer Science | [ SDV.BIBS ] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] | Computational Theory and Mathematics | Quantitative Biology - Quantitative Methods | Discrete Mathematics and Combinatorics | [ INFO.INFO-BI ] Computer Science [cs]/Bioinformatics [q-bio.QM]
International audience; 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.