写一个实现smith waterman algorithm的python程序
时间: 2024-05-14 17:13:17 浏览: 19
好的,以下是一个简单的实现 Smith-Waterman 算法的 Python 代码:
```python
def smith_waterman(seq1, seq2, match=2, mismatch=-1, gap=-1):
m, n = len(seq1), len(seq2)
score = [[0 for j in range(n+1)] for i in range(m+1)]
max_score = 0
max_i, max_j = 0, 0
for i in range(1, m+1):
for j in range(1, n+1):
if seq1[i-1] == seq2[j-1]:
diagonal_score = score[i-1][j-1] + match
else:
diagonal_score = score[i-1][j-1] + mismatch
up_score = score[i-1][j] + gap
left_score = score[i][j-1] + gap
score[i][j] = max(0, diagonal_score, up_score, left_score)
if score[i][j] > max_score:
max_score = score[i][j]
max_i, max_j = i, j
align1, align2 = "", ""
i, j = max_i, max_j
while score[i][j] > 0:
if score[i][j] == score[i-1][j-1] + (match if seq1[i-1] == seq2[j-1] else mismatch):
align1 = seq1[i-1] + align1
align2 = seq2[j-1] + align2
i, j = i-1, j-1
elif score[i][j] == score[i-1][j] + gap:
align1 = seq1[i-1] + align1
align2 = "-" + align2
i -= 1
else:
align1 = "-" + align1
align2 = seq2[j-1] + align2
j -= 1
return max_score, align1, align2
# 示例输入
seq1 = "ATCGGCA"
seq2 = "ATCGCTA"
# 执行 Smith-Waterman 算法
max_score, align1, align2 = smith_waterman(seq1, seq2)
# 输出对齐结果和得分
print("Alignment score:", max_score)
print("Alignment 1:", align1)
print("Alignment 2:", align2)
```
这段代码实现了 Smith-Waterman 算法,可以对两个字符串进行局部比对,并返回一个最高得分和两个对齐的序列。您可以按照需要修改参数来优化这个算法的表现。
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