生物资讯相关演算法文档资料.pptVIP

2003/10/21 Algorithms in Bioinformatics, Lecture 5 生物資訊相關演算法Algorithms in Bioinformatics 呂學一 (中央研究院 資訊科學所) .tw/~hil/ Today Applications of suffix trees Substring problem (暖身) “Exact string matching” revisited Linearization of circular string (挪移乾坤) Longest common substring (異中求同) Intermission – 小巨’s magic show The Lure of Queen (皇后的魅惑) Application One Substring Problem (recap as a warm-up) Substring Problem Input: two strings P and S, where S is allowed to be preprocessed in O(|S|) time. Output: an occurrence of P in S. Objective: done in O(|P|) time. S=bbabbaab S=bbabbaab S=bbabbaab Application Two Exact String Matching Exact String Matching Input: two strings P and S, where S is allowed to be preprocessed in O(|S|) time. Output: all occurrences of P in S. Challenge: solving this in O(|P| + k) time, where k is the number of occurrences of P in S. Idea Each internal node keeps the labels of all its descendant leaves. S=bbabbaab 123456789 S=bbabbaab$ Perhaps not… S = a a a a a $ An observation Consider the sequence L of leaves from left to right. The descendant leaves of each internal node has to be consecutive in L. 123456789 S=bbabbaab$ Application Three Circular String Linearization (挪移乾坤) Notation Let 挪(S, i) denote the string S[i…|S|] S[1…i – 1]. The problem Input a string S. Output an index i that maximizes the alphabetical order of 挪(S, i). 1 2 3 4 5 6 7 8 挪(S,1) = b b a b b a a b 挪(S,2) = b a b b a a b b 挪(S,3) = a b b a a b b b 挪(S,4) = b b a a b b b a 挪(S,5) = b a a b b b a b 挪(S,6) = a a b b b a b b 挪(S,7) = a b b b a b b a 挪(S,8) = b b b a b b a a Na?ve algorithm let j = 1; for i = 2 to |S| do { if (挪(S,i) 挪(S,j)) { let j = i; } } output j; Q: Can we beat O(|S|2)? Linear-Time Algorithm via Suffix Tree First attempt – going right Second Attempt Suffix tree for SS Key observation Each length-|S| substring of SS is a 挪(S, j) for some index j with 1≤ j ≤ |S|. Each 挪(S, j) wit