aa2int - Convert amino acid sequence from letter to integer representation

Syntax

SeqInt = aa2int(SeqChar)

Input Arguments

SeqChar

One of the following: String of 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.

Output Arguments

SeqInt

Amino acid sequence specified by a row vector of integers.

Description

SeqInt = aa2int(SeqChar) converts SeqChar, a character string of 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 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

Converting a Simple Sequence

Convert the sequence of letters MATLAB to integers.

SeqInt = aa2int('MATLAB') 

SeqInt =

   13    1   17   11    1   21

Converting a Random Sequence

1. Create a random string to represent an amino acid sequence.

   SeqChar = randseq(20, 'alphabet', 'amino')
   
   SeqChar =
   
      dwcztecakfuecvifchds

2. Convert the amino acid sequence from letter to integer representation.

   SeqInt = aa2int(SeqChar)
   
   SeqInt =
   
     Columns 1 through 13 
        4  18   5  22  17   7   5   1  12  14   0   7   5
   
     Columns 14 through 20 
       20  10  14   5   9   4  16
   

See Also

aminolookup | int2aa | int2nt | nt2int

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