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Unformatted text preview: SufFx Trees CMSC 423 Preprocessing Strings • Over the next few lectures, we’ll see several methods for preprocessing string data into data structures that make many questions (like searching) easy to answer: • SufFx Tries • SufFx Trees • SufFx Arrays • BorrowsWheeler transform • Typical setting: A long, known, and Fxed text string (like a genome) and many unknown, changing query strings. • Allowed to preprocess the text string once in anticipation of the future unknown queries. • Data structures will be useful in other settings as well. SufFx Tries • A trie , pronounced “try”, is a tree that exploits some structure in the keys e.g. if the keys are strings, a binary search tree would compare the entire strings, but a trie would look at their individual characters SufFx trie are a spaceefFcient data structure to store a string that allows many kinds of queries to be answered quickly. Hugely important for searching large sequences like genomes. The basis for a tool called “MUMMer” (developed by UMD faculty). SufFx Tries s = abaaba$ a b $ $ a $ b a $ a b a $ a b a $ a b a $ SufTrie(s) = sufFx trie representing string s. Edges of the sufFx trie are labeled with letters from the alphabet ∑ (say {A,C,G,T}). Every path from the root to a solid node represents a sufFx of s. Every sufFx of s is represented by some path from the root to a solid node. Why are all the solid nodes leaves? How many leaves will there be? How many nodes can the trie have? Processing Strings Using SufFx Tries • determine whether q is a substring of T? • check whether q is a sufFx of T? • count how many times q appears in T? • Fnd the longest repeat in T? • Fnd the longest common substring of T and q? Given a sufFx trie T, and a string q, how can we: Main idea: every substring of s is a preFx of some sufFx of s. Searching SufFx Tries s = abaaba$ a b $ $ a $ b a $ a b a $ a b a $ a b a $ Is “baa” a substring of s? ¡ollow the path given by the query string. After we’ve built the sufFx trees, queries can be answered in time: O(query) regardless of the text size. Searching SufFx Tries s = abaaba$ a b $ $ a $ b a $ a b a $ a b a $ a b a $ Is “baa” a substring of s? ¡ollow the path given by the query string. After we’ve built the sufFx trees, queries can be answered in time: O(query) regardless of the text size. Applications of SufFx Tries (1) Check whether q is a sufFx of T: Check whether q is a substring of T: Count # of occurrences of q in T: ¡ind the longest repeat in T: ¡ind the lexicographically (alphabetically) Frst sufFx: Applications of SufFx Tries (1) Check whether q is a sufFx of T: Check whether q is a substring of T: ¡ollow the path for q starting from the root....
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.
 Fall '07
 staff

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