Question

Write a code, algorithm for Needleman-wunch and compare

Algorithm:
The algorithm for Needleman wunch in python is as follow.

1st Step
 Define function with seq1 and seq2, and scoring parameters
match score, mismatch penalty, and gap penalty as
parameters.

2nd Step
 Initialize rows and column.
 rows = len(seq1) + 1
 cols = len(seq2) + 1

3rd Step
 Initialize the first row and column of the scoring matrix with
gap penalties:
 For i from 1 to len(seq1):
 score_matrix[i][0] = gap_penalty * i
 For j from 1 to len(seq2):
 score_matrix[0][j] = gap_penalty * j

4th Step
 Now fill remaining matrix
 For i from 1 to rows:
 For j from 1 to coloumn):
 Calculate the scores for match/mismatch and gap:
 If seq1[i-1] equals seq2[j-1]:
 match = score_matrix[i-1] [j-1] + match_score
 Else:
 match = score_matrix[i-1][j-1] + mismatch_penalty
 delete = score_matrix[i-1][j] + gap_penalty
 insert = score_matrix[i][j-1] + gap_penalty
 Consider the maximum among them using maximum pre-
defined function.
5th Step
 Print the matrix.
 for row in score_matrix:
 print(row)

6th Step
 1. Initialize two empty strings, align1 and align2, to store
the aligned sequences.
 2. Set i to the row index of the bottom-right corner of the
scoring matrix.
 3. Set j to the column index of the bottom-right corner of
the scoring matrix.
 4. While i > 0 and j > 0:
 a. If seq1[i - 1] is equal to seq2[j - 1]:
 - Prepend seq1[i - 1] to align1.
 - Prepend seq2[j - 1] to align2.
 - Decrement i and j by 1.
 b. Else if the current score at score_matrix[i][j] is equal
to score_matrix[i - 1][j - 1] + mismatch_penalty:
 - Prepend seq1[i - 1] to align1.
 - Prepend seq2[j - 1] to align2.
 - Decrement i and j by 1.
 c. Else if the current score at score_matrix[i][j] is equal
to score_matrix[i - 1][j] + gap_penalty:
 - Prepend seq1[i - 1] to align1.
 - Prepend a gap symbol "-" to align2.
 - Decrement i by 1.
 d. Else:
 - Prepend a gap symbol "-" to align1.
 - Prepend seq2[j - 1] to align2.
 - Decrement j by 1.
 5. While i > 0:
 - Prepend seq1[i - 1] to align1.
 - Prepend a gap symbol "-" to align2.
 - Decrement i by 1.
 6. While j > 0:
 - Prepend a gap symbol "-" to align1.
 - Prepend seq2[j - 1] to align2.
  - Decrement j by 1.
 7. Return align1 and align2 as the aligned sequences..

Code
def needleman_wunsch(seq1, seq2, match_score=1, mismatch_penalty=-1, gap_penalty=-2):

# Create the scoring matrix

rows = len(seq1) + 1

cols = len(seq2) + 1

score_matrix = [[0] * cols for _ in range(rows)]

# Initialize the first row and column with gap penalties

for i in range(1, rows):

score_matrix[i][0] = gap_penalty * i

for j in range(1, cols):

score_matrix[0][j] = gap_penalty * j

# Fill in the rest of the scoring matrix

for i in range(1, rows):

for j in range(1, cols):

# Calculate the scores for match/mismatch and gap

if seq1[i - 1] == seq2[j - 1]:

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

else:

match = score_matrix[i - 1][j - 1] + mismatch_penalty

delete = score_matrix[i - 1][j] + gap_penalty

insert = score_matrix[i][j - 1] + gap_penalty

# Choose the maximum score

score_matrix[i][j] = max(match, delete, insert)

for row in score_matrix:

print(row)
# Traceback to find the optimal alignment

align1 = ""

align2 = ""

i, j = rows - 1, cols - 1

while i > 0 and j > 0:

if seq1[i - 1] == seq2[j - 1]:

align1 = seq1[i - 1] + align1

align2 = seq2[j - 1] + align2

i -= 1

j -= 1

elif score_matrix[i][j] == score_matrix[i - 1][j - 1] + mismatch_penalty:

align1 = seq1[i - 1] + align1

align2 = seq2[j - 1] + align2

i -= 1

j -= 1

elif score_matrix[i][j] == score_matrix[i - 1][j] + gap_penalty:

align1 = seq1[i - 1] + align1

align2 = "-" + align2

i -= 1

else:

align1 = "-" + align1

align2 = seq2[j - 1] + align2

j -= 1

while i > 0:

align1 = seq1[i - 1] + align1

align2 = "-" + align2

i -= 1

while j > 0:
 align1 = "-" + align1

align2 = seq2[j - 1] + align2

j -= 1

return align1, align2

# Example usage

sequence1 = "CGTATT"

sequence2 = "GACTTT"

alignment1, alignment2 = needleman_wunsch(sequence1, sequence2)

print("Alignment 1:", alignment1)

print("Alignment 2:", alignment2)

Matrix
We have two sequences.
Sequence1=CGTATT
Sequence2=GACTTT
Match score=1
Mismatch=-1
Gap=-2
G A C T T T
0 -2 -4 -6 -8 -10 -12
C -2 -1 -3 -3 -5 -7 -9
G -4 -1 -2 -4 -4 -6 -8
T -6 -3 -2 -3 -3 -3 -5
A -8 -5 -2 -3 -4 -4 -4
T -10 -7 -4 -3 -2 -3 -3
T -12 -9 -6 -5 -2 -1 -2

Sequence1= G A C T T T
Sequence 2= C G T AT T
Score = -2