12_LongestCommonSubsequence.ppt

# 12_LongestCommonSubsequence.ppt - CSC 30155 Wednesday...

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Unformatted text preview: CSC 30155 Wednesday 20/10/10 Dr. Daniel Hughes daniel.hughes@xjtlu.edu.cn Plan for Today l Review of the LCS Problem 20 minutes l A Dynamic LCS Algorithm 30 minutes l LCS questions 40 minutes l Feedback 10 minutes CSC 30155 The Longest Common Subsequence Problem Dr. Daniel Hughes daniel.hughes@xjtlu.edu.cn Supporting Reading l Optional reading: l Cormen et al., Introduction to Algorithms , MIT Press, 2001, Chapter 15: Longest Common Subsequence Problem (15.4) Problem Definition l A subsequence of a given sequence is the given sequence with zero or more elements left out. l Given two sequences: X and Y, we say that a sequence Z is a common subsequence of X and Y if Z is a subsequence of both X and Y. l In the longest common subsequence problem we are given two sequences X and Y and wish to find a maximum-length common subsequence (or LCS) of both X and Y. Comparing to the Longest Common Substring Problem l A string is a sequence of characters. However, a substring is not synonymous with a subsequence. l Substrings are consecutive parts of a string, while subsequences may not be. l From now on, when using the term LCS, we are referring to the Longest Common Subsequence Problem . Example l (b) is a substring and a subsequence of (a): (a) ba babc (b) babc (c) aabc l (c) is a subsequence of (a) but not a substring: (a) b a b abc (b) babc (c) aabc substring subsequence A Key Application: Genetic Identification (1/2) l DNA may be viewed as a text written in the alphabet (A,C,G,T). l Evolution occurs due to a combination of DNA mutation and natural selection. l Mutations include: l Point mutations : replacement of a character. l Insertion mutations : addition of some characters. l Deletion mutations : deletion of some characters. A Key Application: Genetic Identification (2/2) l So if we want to identify the closest genetic relative of an unknown species, we can: l Take a sample of its DNA. l Run LCS against known species. l The one with the longest LCS is probably the closest relative. Why we Need and Efficient LCS Algorithm l While computers grow more powerful, the quantity of information that we want to work with also grows. l The Human Genome has 3 billion base pairs while the Wheat Genome has 17 billion base pairs . l If we want to use LCS to identify a species of wheat, our algorithm will have to be very fast. The Brute-Force Approach l Yesterday you worked on a BRUTE-FORCE algorithm to solve this problem. l The algorithm took two strings as parameters X and Y and: l Enumerated all subsequences in X . l Checked if each subsequence appears in Y . l Returned the longest matching subsequence . Lets Look at the Performance of some implementations: l Java implementations will be uploaded at the end of the week....
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## 12_LongestCommonSubsequence.ppt - CSC 30155 Wednesday...

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