生物资讯相关演算法AlgorithmsinBoinformatics.pptVIP

2003/10/14 Algorithms in Bioinformatics, Lecture 4 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/ Reminder Don’t forget to do Homework 2! Today Constructing suffix tree in linear time. 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: “flaming” Constructing suffix tree in linear time Taking a closer look… Case-1 Step Closer look at Case-1 step Always occurs at a leaf (growing point). At the beginning of iteration k, the path above a leaf has label [?, k–1]. Each Case-1 step in iteration k simply changes the label [?, k–1] to [?, k]. An idea for Case-1 steps Use [?, -] to label the path above each leaf. Thus, no need to do anything for each case-1 step. Taking a closer look… Case-2 Steps: 節外生枝 Closer look at Case-2 step Always occurs at a growing point that is not a leaf, which is not necessarily an internal node. When the growing point is an internal node … Label = [k, -], where k is the current iteration index. Closer look at Case-2 step When the growing point is not an internal node … Taking a closer look… Case-3 Steps: 若無其事 Closer look at Case-3 step Always occurs at a growing point that is not a leaf, which is not necessarily an internal node. When the new position of the growing point is an internal node … Closer look at Case-3 step When the new position of the growing point is not an internal node … Using [?,-] for each leaf Saving a lot of efforts We can simply ignore all Case-1 steps. Recall that the number of Case-2 steps is at most |S|. Q: Is this good enough? Exercise Give a sequence S such that the number of Case-3 steps throughout the process of growing its suffix trie (or suffix tree) is W(|S|2). How does Ukkonen overcome the problem of too many Case-3 (若無其事) steps? Completely ignore them…… 以「若無其事」的態度處理「若無其事」的狀況…… Why Case-3 steps? Why Case-3 steps? For correctly maintaining the position of eac