Question: Need help with my Needleman-Wunsch Python program (traceback) (error)

0

daniel.merlinx •

**0**wrote:Good Afternoon Biostar Community,

I have a problem with my python program. I tried to implement the Needleman-Wunsch algorithm but I get the wrong alignment due to a mistake in the traceback section I assume. I got the correct matrix but not the correct sequence alignment. With this NW("SCHULFACH","SCHLUESSEL","2","-1","-1") input values I should get this solution "SCH_ULFACH || SCHLUESSEL" but I get this "----SCHULFACH and SCHL---UESSEL". It would help me a lot if you have a look at my program and try to figure out what I've done wrong.

Thanks in advance!

def NW(Seq1,Seq2,match,mismatch,gap):

```
#Initialization of the matrix
matrix=[[x for x in range(len(Seq1)+1)] for i in range(len(Seq2)+1)]
#set matrix to zero
for x in range(len(Seq1)+1):
for i in range(len(Seq2)+1):
matrix[i][x]=0
#Calculation of the matrix
traceback=[[x for x in range(len(Seq1)+1)] for i in range(len(Seq2)+1)]
a=0
b=0
if len(Seq1)==len(Seq2):
a=len(Seq1)+1
b=len(Seq2)+1
else:
if len(Seq1)>len(Seq2):
a=len(Seq2)+1
b=len(Seq1)+1
else:
b=len(Seq1)+1
a=len(Seq2)+1
for i in range(a):
for x in range(b):
if x==0 and i==0:
matrix[0][0]=0
else:
if x==0:
f1=float("-inf")
f2=matrix[i-1][x]
f3=float("-inf")
elif i==0:
f1=float("-inf")
f2=float("-inf")
f3=matrix[i][x-1]
else:
f1=matrix[i-1][x-1]
f2=matrix[i][x-1]
f3=matrix[i-1][x]
if(x>0 and i>0):
if(Seq2[i-1]==Seq1[x-1]):
m=int(match)
else:
m=int(mismatch)
else:
m=int(mismatch)
w1=f1+m
w2=f2+int(gap)
w3=f3+int(gap)
erg=(w1,w2,w3)
w4=max(erg)
if w4==w1:
traceback[i][x]=0
elif w4==w2:
traceback[i][x]=1
else:#w4==w3
traceback[i][x]=-1
try:
matrix[i][x]=w4
except IndexError:
print("ERROR")
#traceback
alnseqA=""#horizontal
alnseqB=""#vertical
j=len(Seq1)#horizontal
i=len(Seq2)#vertical
print(j,i)
while(i>0 or j>0):
if traceback[i][j]==0:
alnseqA += Seq1[j-1]
alnseqB += Seq2[i-1]
j=j-1
i=i-1
elif traceback[i][j]==1:
alnseqA += "-"
alnseqB += Seq2[i-1]
i=i-1
else:
alnseqB += "-"
alnseqA += Seq1[j-1]
j=j-1
print(matrix)
print(alnseqA[::-1])
print(alnseqB[::-1])
return (alnseqA,alnseqB)
```

NW("GCTCAA","CTAAG","2","-1","-2")

NW("SCHULFACH","SCHLUESSEL","2","-1","-1")

It seems you're using the wrong scores:

edit: fixed mis-annotation

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