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aminolookup

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

Syntax

aminolookup
aminolookup(SeqAA)
aminolookup('Code', CodeValue)
aminolookup('Integer', IntegerValue)
aminolookup('Abbreviation', AbbreviationValue)
aminolookup('Name', NameValue)

Arguments

SeqAA Character vector of single-letter codes or three-letter abbreviations representing an amino acid sequence. For valid codes and abbreviations, see the table Amino Acid Lookup.
CodeValue Character vector specifying a single-letter code representing an amino acid. For valid single-letter codes, see the table Amino Acid Lookup.
IntegerValueSingle integer representing an amino acid. For valid integers, see the table Amino Acid Lookup.
AbbreviationValue Character vector specifying a three-letter abbreviation representing an amino acid. For valid three-letter abbreviations, see the table Amino Acid Lookup.
NameValue Character vector specifying an amino acid name. For valid amino acid names, see the table Amino Acid Lookup.

Description

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

Amino Acid Lookup

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

aminolookup(SeqAA) converts between single-letter codes and three-letter abbreviations for an amino acid sequence. If the input is a character vector of single-letter codes, then the output is a character character vector of three-letter abbreviations. If the input is a character vector of three-letter abbreviations, then the output is a character vector of the corresponding single-letter codes.

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.

aminolookup('abc')

ans =

AlaAsxCys

aminolookup('Code', CodeValue) displays the corresponding amino acid three-letter abbreviation and name.

aminolookup('Integer', IntegerValue) displays the corresponding amino acid single-letter code, three-letter abbreviation, and name.

aminolookup('Abbreviation', AbbreviationValue) displays the corresponding amino acid single-letter code and name.

aminolookup('Name', NameValue) displays the corresponding amino acid single-letter code and three-letter abbreviation.

Examples

collapse all

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
     '

Introduced before R2006a

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