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序列比对算法-计算生物学

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序列比对算法-计算生物学1 序列比对指将两个或多个序列排列在一起 标明其相似之处

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1.序列比对指将两个或多个序列排列在一起，标明其相似之处。序列中可以插入间隔（通常用短横线“-”表示）。对应的相同或相似的符号（在核酸中是A, T(或U), C, G，在蛋白质中是氨基酸残基的单字母表示）排列在同一列上。这一方法常用于研究由共同祖先进化而来的序列，特别是如蛋白质序列或DNA序列等生物序列。进行相似度分析。
这里写图片描述

2.分类

  • 全局比对：将两个序列中的所有字符都进行依次比对，由于各方面的缺陷，可用性不强。
  • 局部比对（local alignment）：通过动态规划的方式，改动最少来匹配两个序列最相似的部分。
  • 双序列比对：只需要比对两个序列
  • 多序列比对：基于双序列比对，这样，主要是用来提取多个不同序列中，具有的共同特征信息。

3.双序列局部比对。

  • 最大子序列问题，对于两个字符串，通过比较找到两个字符串中相同的子序列，不考虑间隔。
/ 1. Design an algorithm to find the Longest Common Subsequence, Longest Common Substring between two sequences. * Created by zoutai on 2017/10/1. * 从后向前遍历查找，迭代/遍历+动态规划 * 但是递归的方式有一个坏处，就是内部往往那个存在很多重复计算，最大时间复杂度2^n * 所以我们采用空间换时间的办法:直接将所有的L[i][j]遍历出来，时间复杂度即为（mn） */ public class LongestCommonSubsequence { 
    public static void main(String[] args) { String s1 = "AGGTAB"; String s2 = "GXTXAYB"; int m = s1.length(),n=s2.length(); String result = getLongestSubStr(s1,s2,m,n); System.out.println(result); } // 从后向前遍历 public static String getLongestSubStr(String s1,String s2,int m,int n) { if (m == 0 || n == 0) return ""; if (s1.charAt(m - 1) == s2.charAt(n - 1)) return getLongestSubStr(s1, s2, m - 1, n - 1)+s1.charAt(m - 1); else return max(getLongestSubStr(s1, s2, m, n - 1), getLongestSubStr(s1, s2, m - 1, n)); } // 比较字符串长度 public static String max(String a, String b) { if(a==null||b==null){ return ""; } return (a.length() > b.length()) ? a : b; } }
  • Smith-Waterman算法:
    算法主要思想：
    对于A,B两个序列，n,m分别表示他们的长度，构造相应的矩阵和罚分；通过罚分矩阵，得到分数最大的一条路径，即为做好的匹配路径。
    参考链接：wiki
    这里写图片描述
    实现方式：
    • 普通空白函数：
import java.util.LinkedList; import java.util.List; / * Created by zoutai on 2017/10/2. * 2.Tandem repeats. Let P be a pattern of length n and T a text of length m. * Let Pm be the concatenation of P with itself m times, so Pm has length mn. * We want to compute a local alignment between Pm and T . */ public class Alignment02 { 
    public static void main(String[] args) { List<String> list = new LinkedList<String>(); /* 样例1： 输出为： G-CTAGCT GACTA-CT */ String P = new String("AGCT"); String T = new String("GACTACT"); String Pm = new String(); Pm = pToPm(P,T); list = localAlig(Pm,T); /* (不复制)样例2： 输出为： GTT-AC GTTGAC */ // String t1 = new String("TGTTACGG"); // String t2 = new String("GGTTGACTA"); // list = localAlig(t1, t2); for (String str : list) { System.out.println(str.toString()); } } private static List<String> localAlig(String A, String B) { List<String> twoList = new LinkedList<String>(); int allMax = 0; int col = A.length(); int row = B.length(); int[][] mat = new int[row + 1][col + 1]; for (int i = 0; i < col + 1; i++) { mat[0][i] = 0; } for (int j = 0; j < row + 1; j++) { mat[j][0] = 0; } for (int i = 1; i < col+1; i++) { for (int j = 1; j < row+1; j++) { int Match = mat[j - 1][i - 1] + (B.charAt(j-1)==A.charAt(i-1)?3:-3); int Delete = mat[j - 1][i] + (0 - 2); int Insert = mat[j][i - 1] + (0 - 2); mat[j][i] = Math.max(Math.max(Match,0), Math.max(Insert, Delete)); } } // 再次遍历矩阵，获取矩阵最大值，用于查找序列初始点 int tempMax = 0; int temprow =0,tempcol = 0; for (int i =0;i<row+1;i++) { for (int j =0;j<col+1;j++) { System.out.print(mat[i][j]+"."); if (tempMax < mat[i][j]) { tempMax = mat[i][j]; temprow = i; tempcol = j; } } System.out.println(); } String AlignmentA = ""; String AlignmentB = ""; int i = tempcol; int j = temprow; while (i > 0 && j > 0) { if (i > 0 && j > 0 && mat[j][i] == mat[j-1][i-1] + (B.charAt(j-1)==A.charAt(i-1)?3:-3)) { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; i = i - 1; j = j - 1; } else if (i == 1 || j == 1) { break; } else if (j > 0 && mat[j][i] == mat[j - 1][i] + (0 - 2)) { AlignmentA = "-" + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; j = j - 1; } else { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = "-" + AlignmentB; i = i - 1; } } twoList.add(AlignmentA); twoList.add(AlignmentB); return twoList; } // 将p字符串转为pm private static String pToPm(String p, String t) { // TODO Auto-generated method stub int n = p.length(); int m = t.length(); StringBuffer sb = new StringBuffer(); for (int i=0;i<m;i++) { sb.append(p); } return sb.toString(); } } 
* 线性空白函数： 
import java.util.LinkedList; import java.util.List; / * Created by zoutai on 2017/10/2. * Implementation of simple local alignment algorithm * * 线性罚分，Ws=2;Wd=0; */ public class Alignment0301 { 
    public static final int[][] PAM250 = { { 
  4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0}, {-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3}, {-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3}, {-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3}, { 
  0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1}, {-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2}, {-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2}, { 
  0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3}, {-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3}, {-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3}, {-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1}, {-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2}, {-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1}, {-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1}, {-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2}, { 
  1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2}, { 
  0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0}, {-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3}, {-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1}, { 
  0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}}; public static void main(String[] args) { String t1 = new String("TGTTACGG"); String t2 = new String("GGTTGACTA"); List<String> list = new LinkedList<String>(); list = localAlig(t1, t2); for (String str : list) { System.out.println(str.toString()); } } private static List<String> localAlig(String A, String B) { List<String> twoList = new LinkedList<String>(); int allMax = 0; int col = A.length(); int row = B.length(); int[][] mat = new int[row + 1][col + 1]; for (int i = 0; i < col + 1; i++) { mat[0][i] = 0; } for (int j = 0; j < row + 1; j++) { mat[j][0] = 0; } for (int i = 1; i < col+1; i++) { for (int j = 1; j < row+1; j++) { int Match = mat[j - 1][i - 1] + (B.charAt(j-1)==A.charAt(i-1)?3:-3); int Delete = mat[j - 1][i] + (0 - 2); int Insert = mat[j][i - 1] + (0 - 2); mat[j][i] = Math.max(Math.max(Match,0), Math.max(Insert, Delete)); } } // 再次遍历矩阵，获取矩阵最大值，用于查找序列初始点 int tempMax = 0; int temprow =0,tempcol = 0; for (int i =0;i<row+1;i++) { for (int j =0;j<col+1;j++) { System.out.print(mat[i][j]+"."); if (tempMax < mat[i][j]) { tempMax = mat[i][j]; temprow = i; tempcol = j; } } System.out.println(); } String AlignmentA = ""; String AlignmentB = ""; int i = tempcol; int j = temprow; while (i > 1 && j > 1) { if (i > 1 && j > 1 && mat[j][i] == mat[j-1][i-1] + (B.charAt(j-1)==A.charAt(i-1)?3:-3)) { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; i = i - 1; j = j - 1; } else if (i == 1 || j == 1) { break; } else if (j > 1 && mat[j][i] == mat[j - 1][i] + (0 - 2)) { AlignmentA = "-" + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; j = j - 1; } else { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = "-" + AlignmentB; i = i - 1; } } twoList.add(AlignmentA); twoList.add(AlignmentB); return twoList; } } 
* Affine空白函数： 
import java.util.LinkedList; import java.util.List; / * Created by zoutai on 2017/10/2. * Implementation the classical affine-gap local alignment algorithm * * Affine罚分，Ws=2;Wd=10; */ public class Alignment0302 { 
    public static final int[][] PAM250 = { { 
  4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0}, {-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3}, {-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3}, {-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3}, { 
  0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1}, {-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2}, {-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2}, { 
  0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3}, {-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3}, {-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3}, {-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1}, {-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2}, {-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1}, {-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1}, {-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2}, { 
  1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2}, { 
  0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0}, {-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3}, {-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1}, { 
  0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}}; public static void main(String[] args) { String t1 = new String("TGTTACGG"); String t2 = new String("GGTTGACTA"); List<String> list = new LinkedList<String>(); list = localAlig(t1, t2); for (String str : list) { System.out.println(str.toString()); } } private static List<String> localAlig(String A, String B) { List<String> twoList = new LinkedList<String>(); int allMax = 0; int col = A.length(); int row = B.length(); int[][] mat = new int[row + 1][col + 1]; for (int i = 0; i < col + 1; i++) { mat[0][i] = -10; } for (int j = 0; j < row + 1; j++) { mat[j][0] = -10; } for (int i = 1; i < col+1; i++) { for (int j = 1; j < row+1; j++) { int Match = mat[j - 1][i - 1] + Scoring.getScore(PAM250, A.charAt(i - 1), B.charAt(j - 1)); int Delete = mat[j - 1][i] + (0 - 2); int Insert = mat[j][i - 1] + (0 - 2); mat[j][i] = Math.max(Math.max(Match,0), Math.max(Insert, Delete)); } } // 再次遍历矩阵，获取矩阵最大值，用于查找序列初始点 int tempMax = 0; int temprow =0,tempcol = 0; for (int i =0;i<row+1;i++) { for (int j =0;j<col+1;j++) { System.out.print(mat[i][j]+"."); if (tempMax < mat[i][j]) { tempMax = mat[i][j]; temprow = i; tempcol = j; } } System.out.println(); } String AlignmentA = ""; String AlignmentB = ""; int i = tempcol; int j = temprow; while (i > 1 && j > 1) { if (i > 1 && j > 1 && mat[j][i] == mat[j-1][i-1] + Scoring.getScore(PAM250, A.charAt(i - 1), B.charAt(j - 1))) { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; i = i - 1; j = j - 1; } else if (i == 1 || j == 1) { break; } else if (j > 1 && mat[j][i] == mat[j - 1][i] + (0 - 2)) { AlignmentA = "-" + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; j = j - 1; } else { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = "-" + AlignmentB; i = i - 1; } } twoList.add(AlignmentA); twoList.add(AlignmentB); return twoList; } } 
* 其中给定罚分矩阵： 
import java.util.HashMap; //This stores scoring resources, including matrices public class Scoring { //matrix contents are from rosalind: public static final int[][] BLOSUM62 = { { 4, 0, -2, -1, -2, 0, -2, -1, -1, -1, -1, -2, -1, -1, -1, 1, 0, 0, -3, -2}, { 0, 9, -3, -4, -2, -3, -3, -1, -3, -1, -1, -3, -3, -3, -3, -1, -1, -1, -2, -2}, {-2, -3, 6, 2, -3, -1, -1, -3, -1, -4, -3, 1, -1, 0, -2, 0, -1, -3, -4, -3}, {-1, -4, 2, 5, -3, -2, 0, -3, 1, -3, -2, 0, -1, 2, 0, 0, -1, -2, -3, -2}, {-2, -2, -3, -3, 6, -3, -1, 0, -3, 0, 0, -3, -4, -3, -3, -2, -2, -1, 1, 3}, { 0, -3, -1, -2, -3, 6, -2, -4, -2, -4, -3, 0, -2, -2, -2, 0, -2, -3, -2, -3}, {-2, -3, -1, 0, -1, -2, 8, -3, -1, -3, -2, 1, -2, 0, 0, -1, -2, -3, -2, 2}, {-1, -1, -3, -3, 0, -4, -3, 4, -3, 2, 1, -3, -3, -3, -3, -2, -1, 3, -3, -1}, {-1, -3, -1, 1, -3, -2, -1, -3, 5, -2, -1, 0, -1, 1, 2, 0, -1, -2, -3, -2}, {-1, -1, -4, -3, 0, -4, -3, 2, -2, 4, 2, -3, -3, -2, -2, -2, -1, 1, -2, -1}, {-1, -1, -3, -2, 0, -3, -2, 1, -1, 2, 5, -2, -2, 0, -1, -1, -1, 1, -1, -1}, {-2, -3, 1, 0, -3, 0, 1, -3, 0, -3, -2, 6, -2, 0, 0, 1, 0, -3, -4, -2}, {-1, -3, -1, -1, -4, -2, -2, -3, -1, -3, -2, -2, 7, -1, -2, -1, -1, -2, -4, -3}, {-1, -3, 0, 2, -3, -2, 0, -3, 1, -2, 0, 0, -1, 5, 1, 0, -1, -2, -2, -1}, {-1, -3, -2, 0, -3, -2, 0, -3, 2, -2, -1, 0, -2, 1, 5, -1, -1, -3, -3, -2}, { 1, -1, 0, 0, -2, 0, -1, -2, 0, -2, -1, 1, -1, 0, -1, 4, 1, -2, -3, -2}, { 0, -1, -1, -1, -2, -2, -2, -1, -1, -1, -1, 0, -1, -1, -1, 1, 5, 0, -2, -2}, { 0, -1, -3, -2, -1, -3, -3, 3, -2, 1, 1, -3, -2, -2, -3, -2, 0, 4, -3, -1}, {-3, -2, -4, -3, 1, -2, -2, -3, -3, -2, -1, -4, -4, -2, -3, -3, -2, -3, 11, 2}, {-2, -2, -3, -2, 3, -3, 2, -1, -2, -1, -1, -2, -3, -1, -2, -2, -2, -1, 2, 7}}; //This following matrix is copied from rosalind: public static final int[][] PAM250 = { { 
  4,-1,-2,-2,0,-1,-1,0,-2,-1,-1,-1,-1,-2,-1,1,0,-3,-2,0}, {-1,5,0,-2,-3,1,0,-2,0,-3,-2,2,-1,-3,-2,-1,-1,-3,-2,-3}, {-2,0,6,1,-3,0,0,0,1,-3,-3,0,-2,-3,-2,1,0,-4,-2,-3}, {-2,-2,1,6,-3,0,2,-1,-1,-3,-4,-1,-3,-3,-1,0,-1,-4,-3,-3}, { 
  0,-3,-3,-3,9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1}, {-1,1,0,0,-3,5,2,-2,0,-3,-2,1,0,-3,-1,0,-1,-2,-1,-2}, {-1,0,0,2,-4,2,5,-2,0,-3,-3,1,-2,-3,-1,0,-1,-3,-2,-2}, { 
  0,-2,0,-1,-3,-2,-2,6,-2,-4,-4,-2,-3,-3,-2,0,-2,-2,-3,-3}, {-2,0,1,-1,-3,0,0,-2,8,-3,-3,-1,-2,-1,-2,-1,-2,-2,2,-3}, {-1,-3,-3,-3,-1,-3,-3,-4,-3,4,2,-3,1,0,-3,-2,-1,-3,-1,3}, {-1,-2,-3,-4,-1,-2,-3,-4,-3,2,4,-2,2,0,-3,-2,-1,-2,-1,1}, {-1,2,0,-1,-3,1,1,-2,-1,-3,-2,5,-1,-3,-1,0,-1,-3,-2,-2}, {-1,-1,-2,-3,-1,0,-2,-3,-2,1,2,-1,5,0,-2,-1,-1,-1,-1,1}, {-2,-3,-3,-3,-2,-3,-3,-3,-1,0,0,-3,0,6,-4,-2,-2,1,3,-1}, {-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4,7,-1,-1,-4,-3,-2}, { 
  1,-1,1,0,-1,0,0,0,-1,-2,-2,0,-1,-2,-1,4,1,-3,-2,-2}, { 
  0,-1,0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1,1,5,-2,-2,0}, {-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1,1,-4,-3,-2,11,2,-3}, {-2,-2,-2,-3,-2,-1,-2,-3,2,-1,-1,-2,-1,3,-3,-2,-2,2,7,-1}, { 
  0,-3,-3,-3,-1,-2,-2,-3,-3,3,1,-2,1,-1,-2,-2,0,-3,-1,4}}; public static HashMap<Character, Integer> matrixIndex = new HashMap<>(); //initializing values for the matrices, as they are arranged here: static { matrixIndex.put('A', 0); matrixIndex.put('C', 1); matrixIndex.put('D', 2); matrixIndex.put('E', 3); matrixIndex.put('F', 4); matrixIndex.put('G', 5); matrixIndex.put('H', 6); matrixIndex.put('I', 7); matrixIndex.put('K', 8); matrixIndex.put('L', 9); matrixIndex.put('M', 10); matrixIndex.put('N', 11); matrixIndex.put('P', 12); matrixIndex.put('Q', 13); matrixIndex.put('R', 14); matrixIndex.put('S', 15); matrixIndex.put('T', 16); matrixIndex.put('V', 17); matrixIndex.put('W', 18); matrixIndex.put('Y', 19); } // returns the score of a match between the two provided amino acids, as scored by the specified matrix: public static int getScore(int[][] matrix, char reference, char search) { reference = Character.toUpperCase(reference); search = Character.toUpperCase(search); return matrix[matrixIndex.get(reference)][matrixIndex.get(search)]; } } 
* 对文本进行处理测试： 
import java.io.*; import java.util.LinkedList; import java.util.List; / * Created by zoutai on 2017/10/2. */ public class TestAlignment03 { public static final int[][] PAM250 = { { 
  4, -1, -2, -2, 0, -1, -1, 0, -2, -1, -1, -1, -1, -2, -1, 1, 0, -3, -2, 0}, {-1, 5, 0, -2, -3, 1, 0, -2, 0, -3, -2, 2, -1, -3, -2, -1, -1, -3, -2, -3}, {-2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3, 0, -2, -3, -2, 1, 0, -4, -2, -3}, {-2, -2, 1, 6, -3, 0, 2, -1, -1, -3, -4, -1, -3, -3, -1, 0, -1, -4, -3, -3}, { 
  0, -3, -3, -3, 9, -3, -4, -3, -3, -1, -1, -3, -1, -2, -3, -1, -1, -2, -2, -1}, {-1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2, 1, 0, -3, -1, 0, -1, -2, -1, -2}, {-1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3, 1, -2, -3, -1, 0, -1, -3, -2, -2}, { 
  0, -2, 0, -1, -3, -2, -2, 6, -2, -4, -4, -2, -3, -3, -2, 0, -2, -2, -3, -3}, {-2, 0, 1, -1, -3, 0, 0, -2, 8, -3, -3, -1, -2, -1, -2, -1, -2, -2, 2, -3}, {-1, -3, -3, -3, -1, -3, -3, -4, -3, 4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3}, {-1, -2, -3, -4, -1, -2, -3, -4, -3, 2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1}, {-1, 2, 0, -1, -3, 1, 1, -2, -1, -3, -2, 5, -1, -3, -1, 0, -1, -3, -2, -2}, {-1, -1, -2, -3, -1, 0, -2, -3, -2, 1, 2, -1, 5, 0, -2, -1, -1, -1, -1, 1}, {-2, -3, -3, -3, -2, -3, -3, -3, -1, 0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1}, {-1, -2, -2, -1, -3, -1, -1, -2, -2, -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2}, { 
  1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2, 0, -1, -2, -1, 4, 1, -3, -2, -2}, { 
  0, -1, 0, -1, -1, -1, -1, -2, -2, -1, -1, -1, -1, -2, -1, 1, 5, -2, -2, 0}, {-3, -3, -4, -4, -2, -2, -3, -2, -2, -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3}, {-2, -2, -2, -3, -2, -1, -2, -3, 2, -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1}, { 
  0, -3, -3, -3, -1, -2, -2, -3, -3, 3, 1, -2, 1, -1, -2, -2, 0, -3, -1, 4}}; public static void main(String[] args) throws FileNotFoundException,IOException{ File txtFile = new File("data_hm.txt"); BufferedReader br = new BufferedReader(new FileReader(txtFile)); int lineNumber = 0; String line = null; StringBuffer t1 = new StringBuffer(); StringBuffer t2 = new StringBuffer(); List strArr1 = new LinkedList(); List strArr2 = new LinkedList(); int[] resultArr = new int[25]; Boolean first = true; Boolean flag = true; int isget = 1; while ((line = br.readLine())!=null) { if(first) { first = false; continue; } else if(line.equals("")) { first = true; if(isget==2) { strArr1.add(t1); strArr2.add(t2); t1 = new StringBuffer(); t2 = new StringBuffer(); isget--; continue; } isget++; flag = !flag; } else { if(flag) { t1.append(line); } else { t2.append(line); } } } List<String> list = new LinkedList<String>(); System.out.println(strArr1.size()); for (int i =0;i<25;i++) { System.out.println(strArr1.get(i).toString()); System.out.println(strArr2.get(i).toString()); System.out.println(); resultArr[i] = localAlig(strArr1.get(i).toString(), strArr2.get(i).toString()); } System.out.println(resultArr); for (int score: resultArr) { System.out.println(score); } } private static int localAlig(String A, String B) { List<String> twoList = new LinkedList<String>(); int allMax = 0; int col = A.length(); int row = B.length(); int[][] mat = new int[row + 1][col + 1]; for (int i = 0; i < col + 1; i++) { mat[0][i] = -10; } for (int j = 0; j < row + 1; j++) { mat[j][0] = -10; } for (int i = 1; i < col+1; i++) { for (int j = 1; j < row+1; j++) { int Match = mat[j - 1][i - 1] + Scoring.getScore(PAM250, A.charAt(i - 1), B.charAt(j - 1)); int Delete = mat[j - 1][i] + (0 - 2); int Insert = mat[j][i - 1] + (0 - 2); mat[j][i] = Math.max(Math.max(Match,0), Math.max(Insert, Delete)); } } // 再次遍历矩阵，获取矩阵最大值，用于查找序列初始点 int tempMax = 0; int temprow =0,tempcol = 0; for (int i =0;i<row+1;i++) { for (int j =0;j<col+1;j++) { System.out.print(mat[i][j]+"."); if (tempMax < mat[i][j]) { tempMax = mat[i][j]; temprow = i; tempcol = j; } } System.out.println(); } System.out.println(tempMax); String AlignmentA = ""; String AlignmentB = ""; int i = tempcol; int j = temprow; while (i > 1 && j > 1) { if (i > 1 && j > 1 && mat[j][i] == mat[j-1][i-1] + Scoring.getScore(PAM250, A.charAt(i - 1), B.charAt(j - 1))) { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; i = i - 1; j = j - 1; } else if (i == 1 || j == 1) { break; } else if (j > 1 && mat[j][i] == mat[j - 1][i] + (0 - 2)) { AlignmentA = "-" + AlignmentA; AlignmentB = B.charAt(j - 1) + AlignmentB; j = j - 1; } else { AlignmentA = A.charAt(i - 1) + AlignmentA; AlignmentB = "-" + AlignmentB; i = i - 1; } } twoList.add(AlignmentA); twoList.add(AlignmentB); //return twoList; return tempMax; } }

第一题：查找最长子序列
第二题：序列比较算法，使用最普通的方式，Ws = 2, Wd = 0, 无罚分矩阵，默认（相等：不相等）=（+3，-1）
第三题：相对于第二题，添加了罚分矩阵PAM250,(20*20);同时simple local alignment algorithm使用线性罚分，Wd=0,Ws=2;
affine-gap local alignment algorithm使用affine罚分，Wd=10,Ws=2。

第二题：
参考：https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm
https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm#Example

第三题：
参考github用户：https://github.com/hswaffield/Linear-Space-Local-Alignment
http://www.cs.utexas.edu/~mobios/cs329e/rosetta/src/Blosum.java
https://en.wikipedia.org/wiki/Gap_penalty#Affine
https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm#Gap_penalty

相关资料连接链接：http://pan.baidu.com/s/1nvaENdn 密码：gmyf

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