In this paper, we study an efficient index structure, called Suffix Decision Diagrams (SuffixDDs), for knowledge discovery in large sequence data. Recently, Loekito, Bailey, and Pei (KAIS, 2009) proposed a new data structure for sequence data, called Sequence Binary Decision Diagram (SeqBDD), which is an extension of Zero-suppressed Binary Decision Diagrams (ZDDs) for sequences. SuffixDD is a c...

We consider a weighted generalization of multiple sequence alignment with sumof-pair score. Multiple sequence alignment without weights is known to be NPcomplete and can be approximated within a constant factor, but it is unknown whether it has a polynomial time approximation scheme. Weighted multiple sequence alignment can be approximated within a factor of O(log n) where n is the number of se...