生物资讯相关演算法.pptVIP

Na?ve algorithm build suffix tree for B; for L = |A| downto 1 do for i = 1 to |A|-L+1 do { if A[i…i+L-1] occurs in B { output A[i…i+L-1] and halt; } } } output “no common substring”; Time complexity? 2003/10/21 * * 第三十页，共五十四页。 O(|A|3+|B|) ( ) 3 | | 1 2 | | 1 | | 1 | | | | | | ) ( ) 1 | (| A O A i i A O i O i A A L A L A L = ? ? ? ? è ? + - = + - = ? ? ? = = = ? The for-loop takes time Can we do better than this? 2003/10/21 * * 第三十一页，共五十四页。 A faster algorithm build suffix tree for B; for i = 1 to |A| do { find the largest integer L(i) such that A[i…i+L(i)-1] occurs in B by binary search; } output A[i…L(i)] for the i with the largest L(i); Time complexity? 2003/10/21 * * 第三十二页，共五十四页。 O(|A|2 log|A|+|B|) The for-loop takes O(|A|2 log|A|) time. Each binary search takes time O(|A| log |A|). There are overall O(|A|) binary searches. Can we do better than this? 2003/10/21 * * 第三十三页，共五十四页。 Donald E. Knuth conjectured in 1970 that … it is impossible to solve this longest common substring problem in O(|A|+|B|) time. 2003/10/21 * * 第三十四页，共五十四页。 Longest Common Substring in O(|A|+|B|) time via suffix tree 2003/10/21 * * 第三十五页，共五十四页。 Idea Construct a suffix tree T for A#B$, where # and $ are two characters not in A and B. There are exactly |A|+|B|+2 leaves in T, each leaf corresponds to a suffix of A#B$. A-leaf: with label in {1, 2, …, |A|} corresponds to an A-suffix. B-leaf: with label in {|A|+2, …,|A|+|B|+1} corresponds to a B-suffix. $ # A B A-suffix B-suffix 2003/10/21 * * 第三十六页，共五十四页。 Observation Let v be an arbitrary position of T (i.e., v is not necessarily a node of T.) v has a descendant A-leaf if and only if v corresponds to a prefix of an A-suffix of A#B$. v has a descendant B-leaf if and only if v corresponds to a prefix of a B-suffix of A#B$. root v 2003/10/21 * * 第三十七页，共五十四页。 Lemma Let v be a position of T. v has descendant A-leaf and B-suffix if and only if v corresponds to a common substring of A and B. root $ # A B A-suffi