aa2int

Convert amino acid sequence from letter to integer representation

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    Syntax

    SeqInt = aa2int(SeqChar)
    SeqInt = aa2int(SeqChar,Unknown=unknownAA)

    Description

    SeqInt = aa2int(SeqChar) converts a character vector or string containing single-letter codes specifying an amino acid sequence to a row vector of integers specifying the same amino acid sequence. For valid letter codes, see Mapping Amino Acid Letter Codes to Integers.

    example

    SeqInt = aa2int(SeqChar,Unknown=unknownAA) specifies the number used to represent an unknown amino acid.

    Examples

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    Open Live Script

    Create a random amino acid sequence.

    SeqChar = randseq(20,Alphabet="amino")
    SeqChar = 
'TYNYMRQLVVDVVITNHYSV'

    Convert the sequence from letter to integer representation.

    SeqInt = aa2int(SeqChar)
    SeqInt = 1×20 uint8 row vector

   17   19    3   19   13    2    6   11   20   20    4   20   20   10   17    3    9   19   16   20

    Input Arguments

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    Amino acid sequence, specified as one of the following:

    • Character vector or string scalar containing single-letter codes specifying an amino acid sequence. For valid letter codes, see Mapping Amino Acid Letter Codes to Integers. Unknown characters are mapped to 0. Integers are arbitrarily assigned to IUB/IUPAC letters.

    • MATLAB® structure containing a Sequence field that contains an amino acid sequence, such as the output returned by fastaread, getgenpept, genpeptread, getpdb, and pdbread.

    Number representing an unknown amino acid character, specified as a numeric scalar.

    More About

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    Version History

    Introduced before R2006a

    See Also

    Functions