DNA序列局部比对（Smith–Waterman algorithm）

生物信息原理作业第三弹：DNA序列局部比对，利用Smith–Waterman算法，python3.6代码实现。

实例以及原理均来自https://en.wikipedia.org/wiki/Smith%E2%80%93Waterman_algorithm。

DNA序列局部比对

转载请保留出处！

 import numpy as np

 import pandas as pd

 sequence1 = 'TGTTACGG'

 sequence2 = 'GGTTGACTA'

 s1 = ''

 s2 = ''

 gap = -2

 score_matrix = pd.read_excel('score.xlsx')      #匹配得分

 print(score_matrix)

 best_matrix = np.empty(shape= (len(sequence2)+1,len(sequence1)+1),dtype = int)

 def get_match_score(s1,s2):

     score = score_matrix[s1][s2]

     return score

 def get_matrix_max(matrix):                    #得到最大分数下标

     Max = matrix.max()

     for i in range(len(sequence2)+1):

         for j in range(len(sequence1)+1):

             if matrix[i][j] == Max:

                 return (i,j)

 for i in range(len(sequence2)+1):

     for j in range(len(sequence1)+1):

         if i == 0 or j == 0:

             best_matrix[i][j] = 0

         else:

             match = get_match_score(sequence2[i-1],sequence1[j-1])

             gap1_score = best_matrix[i-1][j] + gap

             gap2_score = best_matrix[i][j-1] + gap

             match_score = best_matrix[i-1][j-1]+match

             score = max(gap1_score,gap2_score,match_score)

             if score>0:

                 best_matrix[i][j] = score

             else:

                 best_matrix[i][j] = 0

 print(best_matrix)

 #traceback

 i,j = get_matrix_max(best_matrix)

 while(best_matrix[i][j]!= 0):

     match = get_match_score(sequence2[i-1],sequence1[j-1])

     if i>0 and j>0 and best_matrix[i][j] == best_matrix[i-1][j-1]+match:

         s1 += sequence1[j-1]

         s2 += sequence2[i-1]

         i-=1;j-=1

     elif i>0 and best_matrix[i,j] == best_matrix[i-1,j]+gap:

         s1+='-'

         s2+=sequence2[i-1]

         i-=1

     else:

         s1+=sequence1[j-1]

         s2+='-'

         j-=1

 print(s1[::-1]+'\n'+s2[::-1])

感觉我的得分矩阵写成Excel不必要，等我熟悉一下Numpy和Python命令行之后会修改的。