Suffix Tree and Suffix Array.ppt

Suffix Tree and Suffix Array Outline Motivation Exact Matching Problem Suffix Tree Building issues Suffix Array Build Search Longest common prefixes Extra topics discussion Suffix Tree VS. Suffix Array Exact Matching Problem Find ‘ssi’ in ‘mississippi’ Exact Matching Problem Find ‘ssi’ in ‘mississippi’ Exact Matching Problem Find ‘ssi’ in ‘mississippi’ Exact Matching Problem Find ‘ssi’ in ‘mississippi’ Exact Matching Problem Find ‘sissy’ in ‘mississippi’ Exact Matching Problem Find ‘sissy’ in ‘mississippi’ Exact Matching Problem Find ‘sissy’ in ‘mississippi’ Exact Matching Problem Find ‘sissy’ in ‘mississippi’ Exact Matching Problem So what? Knuth-Morris-Pratt and Boyer-Moore both achieve this worst case bound. O(m+n) when the text and pattern are presented together. Suffix trees are much faster when the text is fixed and known first while the patterns vary. O(m) for single time processing the text, then only O(n) for each new pattern. Aho-Corasick is faster for searching a number of patterns at one time against a single text. Boyer-Moore Algorithm For string matching(exact matching problem) Time complexity O(m+n) for worst case and O(n/m) for absense Method: backward matching with 2 jumping arrays(bad character table and good suffix table) Suffix Tree Properties of a Suffix Tree Each tree edge is labeled by a substring of S. Each internal node has at least 2 children. Each S(i) has its corresponding labeled path from root to a leaf, for 1? i ? n . There are n leaves. No edges branching out from the same internal node can start with the same character. Building the Suffix Tree How do we build a suffix tree? while suffixes remain: add next shortest suffix to the tree Building the Suffix Tree papua Building the Suffix Tree papua Building the Suffix Tree papua Building the Suffix Tree papua Building the Suffix Tree papua Building the Suffix Tree papua Building the Suffix Tree papua Building the Suffix Tree How do we build a suffix tree? while suffixes remain: ad