Suffix Tree of Alignment: An Efficient Index for Similar Data

Abstract: We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has $|A|+|B|$ leaves and can be constructed in $O(|A|+|B|)$ time. However, if the two strings are similar, the generalized suffix tree is not efficient because it does not exploit the similarity which is usually represented as an alignment of $A$ and $B$. In this paper we propose a space/time-efficient suffix tree of alignment which wisely exploits the similarity in an alignment. Our suffix tree for an alignment of $A$ and $B$ has $|A| + l_d + l_1$ leaves where $l_d$ is the sum of the lengths of all parts of $B$ different from $A$ and $l_1$ is the sum of the lengths of some common parts of $A$ and $B$. We did not compromise the pattern search to reduce the space. Our suffix tree can be searched for a pattern $P$ in $O(|P|+occ)$ time where $occ$ is the number of occurrences of $P$ in $A$ and $B$. We also present an efficient algorithm to construct the suffix tree of alignment. When the suffix tree is constructed from scratch, the algorithm requires $O(|A| + l_d + l_1 + l_2)$ time where $l_2$ is the sum of the lengths of other common substrings of $A$ and $B$. When the suffix tree of $A$ is already given, it requires $O(l_d + l_1 + l_2)$ time.