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aa2int

Convert amino acid sequence from letter to integer representation

Syntax

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

Input Arguments

SeqChar

One of the following:

unknownAANumber representing an unknown amino acid. Default is 0.

Output Arguments

SeqIntAmino acid sequence specified by a row vector of integers.

Description

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

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

Mapping Amino Acid Letter Codes to Integers

Amino AcidCodeInteger
Alanine A 1
Arginine R 2
Asparagine N 3
Aspartic acid (Aspartate) D 4
Cysteine C 5
Glutamine Q 6
Glutamic acid (Glutamate) E 7
Glycine G 8
Histidine H 9
Isoleucine I10
Leucine L 11
Lysine K 12
Methionine M 13
Phenylalanine F 14
Proline P 15
SerineS16
ThreonineT17
Tryptophan W 18
Tyrosine Y 19
Valine V 20
Asparagine or Aspartic acid (Aspartate) B 21
Glutamine or Glutamic acid (Glutamate)Z 22
Unknown amino acid (any amino acid) X 23
Translation stop * 24
Gap of indeterminate length - 25
Unknown character (any character or symbol not in table) ? 0

Examples

collapse all

Create a random amino acid sequence.

seq = randseq(20,'alphabet','amino')
seq = 
'TYNYMRQLVVDVVITNHYSV'

Convert the sequence from letter to integer representation.

seqInt = aa2int(seq)
seqInt = 1x20 uint8 row vector

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

Introduced before R2006a