aminolookup

Find amino acid codes, integers, abbreviations, names, and codons

Syntax

aminolookup

conversion = aminolookup(SeqAA)

lookupInfo = aminolookup(Code=aaCode)

lookupInfo = aminolookup(Integer=aaInteger)

lookupInfo = aminolookup(Abbreviation=aaAbbreviation)

lookupInfo = aminolookup(Name=aaName)

Description

aminolookup displays a table of amino acid codes, integers, abbreviations, names, and codons.

conversion = aminolookup(SeqAA) converts between single-letter codes and three-letter abbreviations for an amino acid sequence.

lookupInfo = aminolookup(Code=aaCode) displays the corresponding amino acid three-letter abbreviation and name.

lookupInfo = aminolookup(Integer=aaInteger) displays the corresponding amino acid single-letter code, three-letter abbreviation, and name.

lookupInfo = aminolookup(Abbreviation=aaAbbreviation) displays the corresponding amino acid single-letter code and name.

lookupInfo = aminolookup(Name=aaName) displays the corresponding amino acid single-letter code and three-letter abbreviation.

Examples

Convert an amino acid sequence to single-letter or three-letter abbreviations

Convert an amino acid sequence in single-letter codes to the corresponding three-letter abbreviations.

aminolookup('MWKQAEDIRDIYDF')

ans = 
'MetTrpLysGlnAlaGluAspIleArgAspIleTyrAspPhe'

Convert an amino acid sequence in three-letter abbreviations to the corresponding single-letter codes.

aminolookup('MetTrpLysGlnAlaGluAspIleArgAspIleTyrAspPhe')

ans = 
'MWKQAEDIRDIYDF'

Display the three-letter abbreviation and name for the amino acid corresponding to the single-letter code R.

aminolookup('Code', 'R')

ans = 
    'Arg	Arginine
     '

Display the single-letter code, three-letter abbreviation, and name for the amino acid corresponding to the integer 1.

aminolookup('Integer', 1)

ans = 
    'A	Ala	Alanine
     '

Display the single-letter code and name for the amino acid corresponding to the three-letter abbreviation asn.

aminolookup('Abbreviation', 'asn')

ans = 
    'N	Asparagine
     '

Display the single-letter code and three-letter abbreviation for the amino acid proline.

aminolookup('Name','proline')

ans = 
    'P	Pro
     '

Input Arguments

SeqAA — Amino acid sequence

character vector | string scalar

Amino acid sequence, specified as a character vector or string scalar containing single-letter codes or three-letter abbreviations representing an amino acid sequence.

The following table displays the amino acid codes, integers, abbreviations, names, and codons.

Amino Acid Lookup

Code	Integer	Abbreviation	Amino Acid Name	Codons
A	1	Ala	Alanine	GCU GCC GCA GCG
R	2	Arg	Arginine	CGU CGC CGA CGG AGA AGG
N	3	Asn	Asparagine	AAU AAC
D	4	Asp	Aspartic acid (Aspartate)	GAU GAC
C	5	Cys	Cysteine	UGU UGC
Q	6	Gln	Glutamine	CAA CAG
E	7	Glu	Glutamic acid (Glutamate)	GAA GAG
G	8	Gly	Glycine	GGU GGC GGA GGG
H	9	His	Histidine	CAU CAC
I	10	Ile	Isoleucine	AUU AUC AUA
L	11	Leu	Leucine	UUA UUG CUU CUC CUA CUG
K	12	Lys	Lysine	AAA AAG
M	13	Met	Methionine	AUG
F	14	Phe	Phenylalanine	UUU UUC
P	15	Pro	Proline	CCU CCC CCA CCG
S	16	Ser	Serine	UCU UCC UCA UCG AGU AGC
T	17	Thr	Threonine	ACU ACC ACA ACG
W	18	Trp	Tryptophan	UGG
Y	19	Tyr	Tyrosine	UAU UAC
V	20	Val	Valine	GUU GUC GUA GUG
B	21	Asx	Asparagine or Aspartic acid (Aspartate)	AAU AAC GAU GAC
Z	22	Glx	Glutamine or Glutamic acid (Glutamate)	CAA CAG GAA GAG
X	23	Xaa	Any amino acid	All codons
*	24	END	Termination codon (translation stop)	UAA UAG UGA
-	25	GAP	Gap of unknown length	NA

If you enter one of the ambiguous single-letter codes B, Z, or X, this function displays the corresponding abbreviation for the ambiguous amino acid character.

Example: "abc"

Data Types: char | string

aaCode — Single-letter code representing amino acid

character vector | string scalar

Single-letter code representing an amino acid, specified as a character vector or string scalar. The function displays the corresponding amino acid three-letter abbreviation and name.

Data Types: char | string

aaInteger — Single integer representing amino acid

integer

Single integer representing an amino acid, specified as an integer. The function displays the corresponding amino acid single-letter code, three-letter abbreviation, and name.

Data Types: double

aaAbbreviation — Three-letter abbreviation representing amino acid

character vector | string scalar

Three-letter abbreviation representing an amino acid, specified as a character vector or string scalar. The function displays the corresponding amino acid single-letter code and name.

Data Types: char | string

aaName — Amino Acid Name

character vector | string scalar

Amino acid name, specified as a character vector or string scalar. The function displays the corresponding amino acid single-letter code and three-letter abbreviation.

Data Types: char | string

Output Arguments

conversion — Single letter code or three-letter abbreviation

character vector

Single letter code or three-letter abbreviation for an amino acid sequence, returned as a character vector.

If the input is a character vector or string scalar of single-letter codes, then the output is a character vector of three-letter abbreviations.

If the input is a character vector or string scalar of three-letter abbreviations, then the output is a character vector of the corresponding single-letter codes.

lookupInfo — Corresponding amino acid single-letter code, three-letter abbreviation, and/or name

character vector

Corresponding amino acid single-letter code, three-letter abbreviation, and/or name, returned as a character vector.

Version History

Introduced before R2006a