lec312 - Suffix Trees checkbld Suffix trees Linearized...

Info iconThis preview shows pages 1–4. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: Suffix Trees checkbld Suffix trees Linearized suffix trees Virtual suffix trees checkbld Suffix arrays Enhanced suffix arrays Suffix cactus, suffix vectors, Suffix Trees String any sequence of characters. Substring of string S string composed of characters i through j , i <= j of S . square4 S = cater => ate is a substring. square4 car is not a substring. square4 Empty string is a substring of S . Subsequence Subsequence of string S string composed of characters i 1 < i 2 < < i k of S . square4 S = cater => ate is a subsequence. square4 car is a subsequence. square4 The empty string is a subsequence. String/Pattern Matching You are given a source string S . Answer queries of the form: is the string p i a substring of S ? Knuth-Morris-Pratt (KMP) string matching. square4 O(|S| + | p i |) time per query. square4 O(n|S| + i | p i |) time for n queries. Suffix tree solution. square4 O(|S| + i | p i |) time for n queries. String/Pattern Matching KMP preprocesses the query string p i , whereas the suffix tree method preprocesses the source string S . An application of string matching. square4 Genome project. square4 Databank of strings (gene sequences). square4 Character set is ATGF . square4 Determine if a new sequence is a substring of a databank sequence....
View Full Document

Page1 / 13

lec312 - Suffix Trees checkbld Suffix trees Linearized...

This preview shows document pages 1 - 4. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online