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: Character vector or string containing single-letter codes specifying an amino acid sequence. For valid letter codes, see the table 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 returned by fastaread, getgenpept, genpeptread, getpdb, or pdbread.

unknownAA

Number representing an unknown amino acid. Default is 0.

Output Arguments

SeqInt

Amino 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 Acid	Code	Integer
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	I	10
Leucine	L	11
Lysine	K	12
Methionine	M	13
Phenylalanine	F	14
Proline	P	15
Serine	S	16
Threonine	T	17
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

Convert an amino acid sequence to integer representation

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

Version History

Introduced before R2006a