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Needleman Algo

The document describes the implementation of the Needleman-Wunsch algorithm for global sequence alignment in Python. It includes functions to build an alignment matrix by recursively calculating scores for matches, mismatches and gaps. A directional string is generated from the matrix to trace the optimal alignment. This string is then used to build the alignment by iterating through the characters and concatenating matching/gap characters to the alignment strings.

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Aeman Maqsood
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87 views

Needleman Algo

The document describes the implementation of the Needleman-Wunsch algorithm for global sequence alignment in Python. It includes functions to build an alignment matrix by recursively calculating scores for matches, mismatches and gaps. A directional string is generated from the matrix to trace the optimal alignment. This string is then used to build the alignment by iterating through the characters and concatenating matching/gap characters to the alignment strings.

Uploaded by

Aeman Maqsood
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Code that I implemented:

import ​numpy ​as ​num

def n ​ eedleman(): ​#Initializing all the values and setting up the matrix
s ​ 1 = ​"CACGTAT"
​s2 = ​"CGCA"
​N = ​len​(s1)
M = ​len​(s2)
gap = -​1
​mismatch = -​1
​match = ​1
​matrix = num.zeros((m+​1​,n+​1​))
​#building an alignment matrix
m ​ atrix[​0​][​0​] = ​0
​for ​i ​in ​range​(​1​,N):
matrix[​1​][​0​] = matrix[i-​1​][​0​] + gap
​for ​j ​in ​range​(​1​,M):
matrix[​0​][j] = matrix[​0​][j-​1​] + gap
​for ​i ​in ​range​(​1​,N):
​for ​j ​in ​range​(​1​,M):
​if​(s1[i-​1​] == s2[j-​1​]):
score1 = matrix[i-​1​][j-​1​] + match
​else​:
score1 = matrix[i-​1​][j-​1​] + mismatch
score2 = matrix[i][j-​1​] + gap
score3 = matrix[i-​1​][j] + gap
matrix[i,j] = ​max​(score1,score2,score3)

#creating directional strings


def ​direction(matrix,N,M):
dstring = buildDirectionalString(matrix,N,M)
alignment(matrix,N,M,dstring)

#building alignments using directional string


def ​alignment(matrix,N,M):
seq1pos = N-​1
​seq2pos = M-​1
​dirpos = ​0
​top = ​" "
​bottom = ​" "
​while​(dirpos < ​len​(dstring)):
​if​(dstring[dirpos] == ​'D'​):
top+= s1[seq1pos]
bottom+= s2[seq2pos]
seq1pos-= ​1
​seq2pos-=​1
​elif​(dstring[dirpos]==​'V'​):
top+= s1[seq1pos]
bottom+= ​"-"
​seq1pos-=​1
​else​:
top+=​"-"
​bottom+= s2[seq2pos]
dirpos+=​1

#fucntion to create directional string


def ​buildDirectionalString(matrix,N,M):
dstring = ​""
​currentrow = N
currentcol = M
​while​(currentrow!=​0 ​or ​currentcol!=​0​):
​if​(currentrow==​0​):
dstring+=​"H"
​currentcol+=-​1
​elif​(currentcol==​0​):
dstring+=​"V"
​currentrow+=-​1
​elif​(matrix[currentrow][currentcol-​1​] + ​"-" =​ =matrix[currentrow][currentcol] ):
dstring+=​"H"
​currentcol+=-​1
​elif​(matrix[currentrow-​1​][currentcol] + "
​ -" =​ = matrix[currentrow][currentcol]):
dstring+=​"V"
​currentrow+=-​1
​else​:
dstring+=​"D"
​currentrow+=-​1
​currentcol+=-​1
​return ​dstring

PSEUDOCODE:

// Initialization
Input the two sequences: s1 and s2
N = length of s1
M = length of s2
matrix = array of size[N+1][M+1]
gap = gap score
mismatch = mismatch score
match = match score
// Step 1: Build Alignment Matrix
set matrix[0,0] to 0
for each i from 1 to N, inclusive
matrix[i, 0] = matrix[i-1, 0] + gap
for each j from 1 to M, inclusive
matrix[0, j] = matrix[0, j-1] + gap
for each i from 1 to N, inclusive
for each j from 1 to M, inclusive
if (s1[i-1] equals s2[j-1])
score1 = matrix[i-1, j-1] + match
else
socre1 = matrix[i-1, j-1] + mismatch
score2 = matrix[i, j-1] + gap
score3 = matrix[i-1, j] + gap
matrix[i, j] = max(score1, score2, score3)
// Step 2: Create directional strings
dstring = buildDirectionalString(matrix, N, M)
// Step 3: Build alignments using directional strings
seq1pos = N-1 //position of last character in seq1
seq2pos = M-1 //position of last character in seq2
dirpos = 0
while (dirpos < length of directional string)
if (dstring[dirpos] equals 'D')
align s1[seq1pos] and s2[seq2pos]
subtract 1 from seq1pos and seq2pos
else if (dstring[dirpos] equals 'V')
align s1[seq1pos] and a gap
subtract 1 from seq1pos
else // must be an H
align s2[seq2pos] and a gap
subtract 1 from seq2pos
increment dirpos
//Function to directional string
function buildDirectionalString(matrix, N, M)
dstring = ''
currentrow = N
currentcol = M
while (currentrow != 0 or currentcol != 0)
if (currentrow is 0)
add 'H' to dstring
subtract 1 from currentcol
else if (currentcol is 0)
add 'V' to dstring
subtract 1 from currentrow
else if (matrix[currentrow, currentcol-1] + gap equals matrix[currentrow,
currentcol])
add 'H' to dstring
subtract 1 from currentcol
else if (matrix[currentrow-1, currentcol] + gap equals matrix[currentrow,
currentcol])
add 'V' to dstring
subtract 1 from currentrow
else
add 'D' to dstring
subtract 1 from currentrow
subtract 1 from currentcol
return dstring

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