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aa2int

Convert amino acid sequence from letter to integer representation

Syntax

SeqInt = aa2int(SeqChar)

Input Arguments

SeqChar

One of the following:

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.

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