Q1 a Write a program to construct a dot plot for the alignment of human and

chicken+haemoglobin β chain. Identify the segments, which are same in both sequences.

M V H W T A E E K Q L I T G L W G K V N V A E C G A E A L A R L L I V Y P W T Q R F F A S F G N L S S P T A I L G N P M V R A H G K K V L T S F G D A V K N L D N I K N T F S Q L S E L H C D K L H V D P E N F R L L G D I L I I V L A A H F S K D F T P E C Q A A W Q K L V R V V A H A L A R K Y H
M . .
V . . . . . . . . . . . .
H . . . . . . .
L . . . . . . . . . . . . . . . . . .
T . . . . . . .
P . . . . .
E . . . . . . .
E . . . . . . .
K . . . . . . . . . .
S . . . . . . .
A . . . . . . . . . . . . . . .
V . . . . . . . . . . .
T . . . . . . .
A . . . . . . . . . . . . . . .
L . . . . . . . . . . . . . . . . .
W . . .
G . . . . . . .
K . . . . . . . . . .
V . . . . . . . . . . . .
N . . . . . . .
V . . . . . . . . . . . .
D . . . . . .
E . . . . . . .
V . . . . . . . . .
G . . . . . . .
G . . . . . .
E . . . . . . .
A . . . . . . . . . . . . .
L . . . . . . . . . . . . . . . . .
G . . . . . .
R . . . . . .
L . . . . . . . . . . . . . . . . .
L . . . . . . . . . . . . . . . . .
V . . . . . . . . .
V . . . . . . . . . . . .
Y . .
P . . . . .
W . . .
T . . . . . . .
Q . . . .
R . . . . . .
F . . . . . . . .
F . . . . . . . .
E . . .
S . . . . . . .
F . . . . . . . .
G . . . . . . .
D . . . . . .
L . . . . . . . . . . . . . . . . .
S . . . . . . .
T . . . .
P . . . . .
D . . . . . .
A . . . . . . . . . . .
V . . . . . . . .
M .
G . . . . . . .
N . . . . . .
P . . . . .
K . . . . . . . .
V . . . . . . . . . . . .
K . . . . . . . .
A . . . . . . . . . . .
H . . . . . . .
G . . . . . . .
K . . . . . . . . . .
K . . . . . . . . . .
V . . . . . . . . . . . .
L . . . . . . . . . . . . . . . .
G . .
A . . . . . . . .
F . . . . . . . .
S . . .
D . . . . . .
G . .
L . . . . . . . . . .
A . . . . . . .
H . . . . .
L . . . . . . . . . . . . . . . .
D . . . . . .
N . . . . .
L . . . . . . . . .
K . . . . . . . . .
G .
T . . . . .
F . . . . . . . .
A . . . . . . .
T .
L . . . . . . . . . . . . . . . .
S . . . .
E . . . . . . .
L . . . . . . . . . . . . . . . .
H . . . . . . .
C . .
D . . . . . .
K . . . . . . . . .
L . . . . . . . . . . . . . . . .
H . . . . . . .
V . . . . . . . . . . .
D . . . . . .
P . . . . .
E . . . . . . .
N . . . .
F . . . . . . . .
R . . . . .
L . . . . . . . . . . . . . . . .
L . . . . . . . . . . . . . . . .
G . . . . . .
N .
V . . . .
L . . . . . . . . . . . . . . . .
V . . . .
C .
V . . . . . . . . . . .
L . . . . . . . . . . . . . . . .
A . . . . . . . . . .
H . . .
H . . . . . . .
F . . . . . . . .
G .
K . . . . . . . . .
E .
F . . . . . . . .
T . . . . .
P . . . . .
P
V . . .
Q . . .
A . . . . . . . . .
A . . . . . . . . .
Y .
Q . . .
K . . . . . . . . .
V . . . .
V . . . . . . . . . . .
A . . .
G
V . . . . . . . . . .
A . . . . . . . . .
N .
A . . . . . . . . .
L . . . . . . . . . . . . . . .
A . . . . . . . . .
H .
K . . . . . . . . .
Y . .
H . . . . . .
Segments which are same in both sequence
MVH (1 to 3)*
EEK (7 to 9)*
LWGKVNV (15 to 21)
VYPWTQRFF (35 to 43)
AHGKKVL (63 to 69)
LSELHCDKLHVDPENFRLLG (89 to 108)

b. Construct the dot plot manually for the residues 1-20 and verify with the plot
obtained using program
> Verified and found similarity between program and manual plot
2.Calculate the score for the following alignments using code:
AATCTATA
AAG--ATA

AATCTATA
AAG--ATA
Q 3
=5*(1) +2(-1) + 1 (-2)= 1
The alignment score manually is 1 which verifies the code.

Q4 Using the Needleman and Wunsch dynamic programming method, construct

the partial alignment score table and align the following two sequences
(using code):
ACAGTCGAACG and ACCGTCCG

# define the sequences

seq1 = "ACAGTCGAACG"
seq2 = "ACCGTCCG"

# define the scoring parameters

match_score = 2
mismatch_score = -1
gap_penalty = -2

# create the score matrix

score_matrix = [[0 for j in range(len(seq2) + 1)] for i in range(len(seq1)
+ 1)]

# initialize the first row and column of the score matrix

for i in range(len(seq1) + 1):
score_matrix[i][0] = i * gap_penalty
for j in range(len(seq2) + 1):
score_matrix[0][j] = j * gap_penalty

# fill in the rest of the score matrix using dynamic programming

for i in range(1, len(seq1) + 1):
for j in range(1, len(seq2) + 1):
match = score_matrix[i-1][j-1] + (match_score if seq1[i-1] ==
seq2[j-1] else mismatch_score)
delete = score_matrix[i-1][j] + gap_penalty
insert = score_matrix[i][j-1] + gap_penalty
score_matrix[i][j] = max(match, delete, insert)
# initialize the indices to the bottom-right corner of the score matrix
i, j = len(seq1), len(seq2)

# initialize the aligned sequences as empty strings

aligned_seq1 = ""
aligned_seq2 = ""

# backtrack through the score matrix to obtain the aligned sequences

while i > 0 or j > 0:
if i > 0 and j > 0 and score_matrix[i][j] == score_matrix[i-1][j-1] +
(match_score if seq1[i-1] == seq2[j-1] else mismatch_score):
aligned_seq1 = seq1[i-1] + aligned_seq1
aligned_seq2 = seq2[j-1] + aligned_seq2
i -= 1
j -= 1
elif i > 0 and score_matrix[i][j] == score_matrix[i-1][j] +
gap_penalty:
aligned_seq1 = seq1[i-1] + aligned_seq1
aligned_seq2 = "-" + aligned_seq2
i -= 1
else:
aligned_seq1 = "-" + aligned_seq1
aligned_seq2 = seq2[j-1] + aligned_seq2
j -= 1

# print the aligned sequences

print("Aligned Sequence 1: " + aligned_seq1)
print("Aligned Sequence 2: " + aligned_seq2)

Output
Q 5

Maximum score is 7