动态规划法——双序列比对.ppt

* /55 Local Alignment: Example * /55 Local Alignment: Example * /55 Local Alignment: Example * /55 Local Alignment: Example * /55 Local Alignment: Running Time Long run time O(n4): - In the grid of size n x n there are ~n2 vertices (i,j) that may serve as a source. - For each such vertex computing alignments from (i,j) to (i’,j’) takes O(n2) time. This can be remedied by giving free rides * /55 Local Alignment: Free Rides Vertex (0,0) The dashed edges represent the free rides from (0,0) to every other node. Yeah, a free ride! * /55 The Local Alignment Recurrence The largest value of si,j over the whole edit graph is the score of the best local alignment. The recurrence: 0 si,j = max si-1,j-1 + δ (vi, wj) s i-1,j + δ (vi, -) s i,j-1 + δ (-, wj) Notice there is only this change from the original recurrence of a Global Alignment * /55 The Local Alignment Recurrence The largest value of si,j over the whole edit graph is the score of the best local alignment. The recurrence: 0 si,j = max si-1,j-1 + δ (vi, wj) s i-1,j + δ (vi, -) s i,j-1 + δ (-, wj) Power of ZERO: there is only this change from the original recurrence of a Global Alignment - since there is only one “free ride” edge entering into every vertex * /55 /Blast.cgi NP_006735 NP_000945 * /55 * /55 习题 考虑序列v=TACGGGTAT和w= GGACGTACG。假设匹配奖励+1，错配和插缺罚分均为-1. 【作业】 填写序列v和w之间的全局联配的动态规划表（编辑图或相似度矩阵）。在各单元画出箭头以存储返回信息。全局最优联配的得分是多少？这个得分对应的联配又是什么？ 填写序列v和w之间的局部联配的动态规划表。在各单元画出箭头以存储返回信息。在这种情形下，局部最优联配的得分是多少？这个得分对应的联配又是什么？ * /55 - 0 1 2 3 4 5 6 7 8 9 0 0 -1 -2 -3 -4 -5 -6 -7 -8 -9 1 -1 2 -2 3 -3 4 -4 5 -5 6 -6 7 -7 8 -8 9 9 G G A C G T A C G T A C G G G T A T 全局比对 * /55 局部比对 - 0 1 2 3 4 5 6 7 8 9 0 0 0 0 0 0 0 0 0 0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 0 G G A C G T A C G T A C G G G T A T * /55 Scoring Indels: Naive Approach A fixed penalty σ is given to every indel: -σ f