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    Needleman Algo

    Uploaded by

    Aeman Maqsood
    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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    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd

    Needleman Algo

    Uploaded by

    Aeman Maqsood
    76 views4 pages
    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.

    Original Description:

    global alignment

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    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.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    76 views4 pages

    Needleman Algo

    Uploaded by

    Aeman Maqsood
    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.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 4

    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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