BLOSUM62 in Python
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2.8 years ago

Hi, how can i implement the BLOSUM62 matrix in Python without modules like Scikit-Bio or Bio? Can someone give me an hand? Thanks.

alignment blosum62 python python3 needleman-wunsch • 13k views
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What do you mean by 'implement' the matrix? A matrix is just a list of lists essentially.

In any event, the first google hit for 'blosum62 python' is:

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7 months ago

There is a super small python module called blosum. It does exactly that: https://pypi.org/project/blosum/

import blosum as bl

mat = bl.BLOSUM(62)    
valueXY = mat["XY"]

If you want it as dictionary just do:

blosumDict = dict(mat)
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2.8 years ago
blosum62 = {
    ('W', 'F'): 1, ('L', 'R'): -2, ('S', 'P'): -1, ('V', 'T'): 0,
    ('Q', 'Q'): 5, ('N', 'A'): -2, ('Z', 'Y'): -2, ('W', 'R'): -3,
    ('Q', 'A'): -1, ('S', 'D'): 0, ('H', 'H'): 8, ('S', 'H'): -1,
    ('H', 'D'): -1, ('L', 'N'): -3, ('W', 'A'): -3, ('Y', 'M'): -1,
    ('G', 'R'): -2, ('Y', 'I'): -1, ('Y', 'E'): -2, ('B', 'Y'): -3,
    ('Y', 'A'): -2, ('V', 'D'): -3, ('B', 'S'): 0, ('Y', 'Y'): 7,
    ('G', 'N'): 0, ('E', 'C'): -4, ('Y', 'Q'): -1, ('Z', 'Z'): 4,
    ('V', 'A'): 0, ('C', 'C'): 9, ('M', 'R'): -1, ('V', 'E'): -2,
    ('T', 'N'): 0, ('P', 'P'): 7, ('V', 'I'): 3, ('V', 'S'): -2,
    ('Z', 'P'): -1, ('V', 'M'): 1, ('T', 'F'): -2, ('V', 'Q'): -2,
    ('K', 'K'): 5, ('P', 'D'): -1, ('I', 'H'): -3, ('I', 'D'): -3,
    ('T', 'R'): -1, ('P', 'L'): -3, ('K', 'G'): -2, ('M', 'N'): -2,
    ('P', 'H'): -2, ('F', 'Q'): -3, ('Z', 'G'): -2, ('X', 'L'): -1,
    ('T', 'M'): -1, ('Z', 'C'): -3, ('X', 'H'): -1, ('D', 'R'): -2,
    ('B', 'W'): -4, ('X', 'D'): -1, ('Z', 'K'): 1, ('F', 'A'): -2,
    ('Z', 'W'): -3, ('F', 'E'): -3, ('D', 'N'): 1, ('B', 'K'): 0,
    ('X', 'X'): -1, ('F', 'I'): 0, ('B', 'G'): -1, ('X', 'T'): 0,
    ('F', 'M'): 0, ('B', 'C'): -3, ('Z', 'I'): -3, ('Z', 'V'): -2,
    ('S', 'S'): 4, ('L', 'Q'): -2, ('W', 'E'): -3, ('Q', 'R'): 1,
    ('N', 'N'): 6, ('W', 'M'): -1, ('Q', 'C'): -3, ('W', 'I'): -3,
    ('S', 'C'): -1, ('L', 'A'): -1, ('S', 'G'): 0, ('L', 'E'): -3,
    ('W', 'Q'): -2, ('H', 'G'): -2, ('S', 'K'): 0, ('Q', 'N'): 0,
    ('N', 'R'): 0, ('H', 'C'): -3, ('Y', 'N'): -2, ('G', 'Q'): -2,
    ('Y', 'F'): 3, ('C', 'A'): 0, ('V', 'L'): 1, ('G', 'E'): -2,
    ('G', 'A'): 0, ('K', 'R'): 2, ('E', 'D'): 2, ('Y', 'R'): -2,
    ('M', 'Q'): 0, ('T', 'I'): -1, ('C', 'D'): -3, ('V', 'F'): -1,
    ('T', 'A'): 0, ('T', 'P'): -1, ('B', 'P'): -2, ('T', 'E'): -1,
    ('V', 'N'): -3, ('P', 'G'): -2, ('M', 'A'): -1, ('K', 'H'): -1,
    ('V', 'R'): -3, ('P', 'C'): -3, ('M', 'E'): -2, ('K', 'L'): -2,
    ('V', 'V'): 4, ('M', 'I'): 1, ('T', 'Q'): -1, ('I', 'G'): -4,
    ('P', 'K'): -1, ('M', 'M'): 5, ('K', 'D'): -1, ('I', 'C'): -1,
    ('Z', 'D'): 1, ('F', 'R'): -3, ('X', 'K'): -1, ('Q', 'D'): 0,
    ('X', 'G'): -1, ('Z', 'L'): -3, ('X', 'C'): -2, ('Z', 'H'): 0,
    ('B', 'L'): -4, ('B', 'H'): 0, ('F', 'F'): 6, ('X', 'W'): -2,
    ('B', 'D'): 4, ('D', 'A'): -2, ('S', 'L'): -2, ('X', 'S'): 0,
    ('F', 'N'): -3, ('S', 'R'): -1, ('W', 'D'): -4, ('V', 'Y'): -1,
    ('W', 'L'): -2, ('H', 'R'): 0, ('W', 'H'): -2, ('H', 'N'): 1,
    ('W', 'T'): -2, ('T', 'T'): 5, ('S', 'F'): -2, ('W', 'P'): -4,
    ('L', 'D'): -4, ('B', 'I'): -3, ('L', 'H'): -3, ('S', 'N'): 1,
    ('B', 'T'): -1, ('L', 'L'): 4, ('Y', 'K'): -2, ('E', 'Q'): 2,
    ('Y', 'G'): -3, ('Z', 'S'): 0, ('Y', 'C'): -2, ('G', 'D'): -1,
    ('B', 'V'): -3, ('E', 'A'): -1, ('Y', 'W'): 2, ('E', 'E'): 5,
    ('Y', 'S'): -2, ('C', 'N'): -3, ('V', 'C'): -1, ('T', 'H'): -2,
    ('P', 'R'): -2, ('V', 'G'): -3, ('T', 'L'): -1, ('V', 'K'): -2,
    ('K', 'Q'): 1, ('R', 'A'): -1, ('I', 'R'): -3, ('T', 'D'): -1,
    ('P', 'F'): -4, ('I', 'N'): -3, ('K', 'I'): -3, ('M', 'D'): -3,
    ('V', 'W'): -3, ('W', 'W'): 11, ('M', 'H'): -2, ('P', 'N'): -2,
    ('K', 'A'): -1, ('M', 'L'): 2, ('K', 'E'): 1, ('Z', 'E'): 4,
    ('X', 'N'): -1, ('Z', 'A'): -1, ('Z', 'M'): -1, ('X', 'F'): -1,
    ('K', 'C'): -3, ('B', 'Q'): 0, ('X', 'B'): -1, ('B', 'M'): -3,
    ('F', 'C'): -2, ('Z', 'Q'): 3, ('X', 'Z'): -1, ('F', 'G'): -3,
    ('B', 'E'): 1, ('X', 'V'): -1, ('F', 'K'): -3, ('B', 'A'): -2,
    ('X', 'R'): -1, ('D', 'D'): 6, ('W', 'G'): -2, ('Z', 'F'): -3,
    ('S', 'Q'): 0, ('W', 'C'): -2, ('W', 'K'): -3, ('H', 'Q'): 0,
    ('L', 'C'): -1, ('W', 'N'): -4, ('S', 'A'): 1, ('L', 'G'): -4,
    ('W', 'S'): -3, ('S', 'E'): 0, ('H', 'E'): 0, ('S', 'I'): -2,
    ('H', 'A'): -2, ('S', 'M'): -1, ('Y', 'L'): -1, ('Y', 'H'): 2,
    ('Y', 'D'): -3, ('E', 'R'): 0, ('X', 'P'): -2, ('G', 'G'): 6,
    ('G', 'C'): -3, ('E', 'N'): 0, ('Y', 'T'): -2, ('Y', 'P'): -3,
    ('T', 'K'): -1, ('A', 'A'): 4, ('P', 'Q'): -1, ('T', 'C'): -1,
    ('V', 'H'): -3, ('T', 'G'): -2, ('I', 'Q'): -3, ('Z', 'T'): -1,
    ('C', 'R'): -3, ('V', 'P'): -2, ('P', 'E'): -1, ('M', 'C'): -1,
    ('K', 'N'): 0, ('I', 'I'): 4, ('P', 'A'): -1, ('M', 'G'): -3,
    ('T', 'S'): 1, ('I', 'E'): -3, ('P', 'M'): -2, ('M', 'K'): -1,
    ('I', 'A'): -1, ('P', 'I'): -3, ('R', 'R'): 5, ('X', 'M'): -1,
    ('L', 'I'): 2, ('X', 'I'): -1, ('Z', 'B'): 1, ('X', 'E'): -1,
    ('Z', 'N'): 0, ('X', 'A'): 0, ('B', 'R'): -1, ('B', 'N'): 3,
    ('F', 'D'): -3, ('X', 'Y'): -1, ('Z', 'R'): 0, ('F', 'H'): -1,
    ('B', 'F'): -3, ('F', 'L'): 0, ('X', 'Q'): -1, ('B', 'B'): 4
}
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1
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Andrzej , you are missing several combinations in your dictionary. (F, Y) for example.

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Oops I did it again. Thank you for pointing that out, Pedro.

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You can then transform this dictionary into a list or NumPy's array.

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