用python编写needleman算法
时间: 2024-02-28 07:26:41 浏览: 14
以下是Python中实现Needleman-Wunsch算法的示例代码:
```
import numpy as np
def needleman_wunsch(seq1, seq2, match=1, mismatch=-1, gap=-1):
n = len(seq1)
m = len(seq2)
score_matrix = np.zeros((n+1, m+1))
for i in range(n+1):
score_matrix[i][0] = i * gap
for j in range(m+1):
score_matrix[0][j] = j * gap
for i in range(1, n+1):
for j in range(1, m+1):
if seq1[i-1] == seq2[j-1]:
score = match
else:
score = mismatch
score_matrix[i][j] = max(score_matrix[i-1][j-1] + score,
score_matrix[i-1][j] + gap,
score_matrix[i][j-1] + gap)
align1 = ""
align2 = ""
i = n
j = m
while i > 0 and j > 0:
score_current = score_matrix[i][j]
score_diagonal = score_matrix[i-1][j-1]
score_up = score_matrix[i][j-1]
score_left = score_matrix[i-1][j]
if score_current == score_diagonal + match:
align1 += seq1[i-1]
align2 += seq2[j-1]
i -= 1
j -= 1
elif score_current == score_left + gap:
align1 += seq1[i-1]
align2 += "-"
i -= 1
elif score_current == score_up + gap:
align1 += "-"
align2 += seq2[j-1]
j -= 1
while i > 0:
align1 += seq1[i-1]
align2 += "-"
i -= 1
while j > 0:
align1 += "-"
align2 += seq2[j-1]
j -= 1
align1 = align1[::-1]
align2 = align2[::-1]
return align1, align2, score_matrix[n][m]
```
该函数接受两个字符串作为输入并返回它们的最佳对齐,以及对齐的分数。默认情况下,匹配得分为1,不匹配得分为-1,间隙得分为-1。可以通过指定参数来更改这些分数。在实现中,我们使用了一个二维矩阵来存储每个位置的得分,并使用回溯来构建最佳对齐。