Bioinformatics Toolbox™

aa2nt - Convert amino acid sequence to nucleotide sequence

Syntax

SeqNT = aa2nt(SeqAA) SeqNT = aa2nt(SeqAA, ...'GeneticCode', GeneticCodeValue, ...) SeqNT = aa2nt(SeqAA, ...'Alphabet' AlphabetValue, ...)

Arguments

SeqAA

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.
Row vector of integers specifying an amino acid sequence. For valid integers, see the table Mapping Amino Acid Integers to Letter Codes.
MATLAB structure containing a Sequence field that contains an amino acid sequence, such as returned by fastaread, getgenpept, genpeptread, getpdb, or pdbread.

Examples: 'ARN' or [1 2 3]

GeneticCodeValue

Integer or string specifying a genetic code number or code name from the table Genetic Code. Default is 1 or 'Standard'.

Tip If you use a code name, you can truncate the name to the first two letters of the name.

AlphabetValue

String specifying a nucleotide alphabet. Choices are:

'DNA' (default) — Uses the symbols A, C, G, and T.
'RNA' — Uses the symbols A, C, G, and U.

Return Values

SeqNT Nucleotide sequence specified by a character string of letter codes.

Description

SeqNT = aa2nt(SeqAA) converts an amino acid sequence, specified by SeqAA, to a nucleotide sequence, returned in SeqNT, using the standard genetic code.

In general, the mapping from an amino acid to a nucleotide codon is not a one-to-one mapping. For amino acids with multiple possible nucleotide codons, this function randomly selects a codon corresponding to that particular amino acid. For the ambiguous characters B and Z, one of the amino acids corresponding to the letter is selected randomly, and then a codon sequence is selected randomly. For the ambiguous character X, a codon sequence is selected randomly from all possibilities.

SeqNT = aa2nt(SeqAA, ...'PropertyName', PropertyValue, ...) calls aa2nt with optional properties that use property name/property value pairs. You can specify one or more properties in any order. Each PropertyName must be enclosed in single quotation marks and is case insensitive. These property name/property value pairs are as follows:

SeqNT = aa2nt(SeqAA, ...'GeneticCode', GeneticCodeValue, ...) specifies a genetic code to use when converting an amino acid sequence to a nucleotide sequence. GeneticCodeValue can be an integer or string specifying a code number or code name from the table Genetic Code. Default is 1 or 'Standard'. The amino acid to nucleotide codon mapping for the Standard genetic code is shown in the table Standard Genetic Code.

Tip If you use a code name, you can truncate the name to the first two letters of the name.

SeqNT = aa2nt(SeqAA, ...'Alphabet' AlphabetValue, ...) specifies a nucleotide alphabet. AlphabetValue can be 'DNA', which uses the symbols A, C, G, and T, or 'RNA', which uses the symbols A, C, G, and U. Default is 'DNA'.

Genetic Code

Code Number	Code Name
`1`	`Standard`
`2`	`Vertebrate Mitochondrial`
`3`	`Yeast Mitochondrial`
`4`	`Mold`, `Protozoan`, `Coelenterate Mitochondrial`, and `Mycoplasma/Spiroplasma`
`5`	`Invertebrate Mitochondrial`
`6`	`Ciliate`, `Dasycladacean`, and `Hexamita Nuclear`
`9`	`Echinoderm Mitochondrial`
`10`	`Euplotid Nuclear`
`11`	`Bacterial` and `Plant Plastid`
`12`	`Alternative Yeast Nuclear`
`13`	`Ascidian Mitochondrial`
`14`	`Flatworm Mitochondrial`
`15`	`Blepharisma Nuclear`
`16`	`Chlorophycean Mitochondrial`
`21`	`Trematode Mitochondrial`
`22`	`Scenedesmus Obliquus Mitochondrial`
`23`	`Thraustochytrium Mitochondrial`

Standard Genetic Code

Amino Acid Name	Amino Acid Code	Nucleotide Codon
Alanine	`A`	`GCT GCC GCA GCG`
Arginine	`R`	`CGT CGC CGA CGG AGA AGG`
Asparagine	`N`	`ATT AAC`
Aspartic acid (Aspartate)	`D`	`GAT GAC`
Cysteine	`C`	`TGT TGC`
Glutamine	`Q`	`CAA CAG`
Glutamic acid (Glutamate)	`E`	`GAA GAG`
Glycine	`G`	`GGT GGC GGA GGG`
Histidine	`H`	`CAT CAC`
Isoleucine	`I`	`ATT ATC ATA`
Leucine	`L`	`TTA TTG CTT CTC CTA CTG`
Lysine	`K`	`AAA AAG`
Methionine	`M`	`ATG`
Phenylalanine	`F`	`TTT TTC`
Proline	`P`	`CCT CCC CCA CCG`
Serine	`S`	`TCT TCC TCA TCG AGT AGC`
Threonine	`T`	`ACT ACC ACA ACG`
Tryptophan	`W`	`TGG`
Tyrosine	`Y`	`TAT, TAC`
Valine	`V`	`GTT GTC GTA GTG`
Asparagine or Aspartic acid (Aspartate)	`B`	Random codon from `D` and `N`
Glutamine or Glutamic acid (Glutamate)	`Z`	Random codon from `E` and `Q`
Unknown amino acid (any amino acid)	`X`	Random codon
Translation stop	`*`	`TAA TAG TGA`
Gap of indeterminate length	`-`	`---`
Unknown character (any character or symbol not in table)	`?`	`???`

Examples

Convert an amino acid sequence to a nucleotide sequence using the standard genetic code.
```
aa2nt('MATLAP')

ans =

ATGGCGACGTTAGCGCCG
```
Convert an amino acid sequence to a nucleotide sequence using the Vertebrate Mitochondrial genetic code.
```
aa2nt('MATLAP', 'GeneticCode', 2)

ans =

ATGGCAACTCTAGCGCCT
```
Convert an amino acid sequence to a nucleotide sequence using the Echinoderm Mitochondrial genetic code and the RNA alphabet.
```
aa2nt('MATLAP','GeneticCode','ec','Alphabet','RNA')

ans =

AUGGCCACAUUGGCACCU
```

Convert an amino acid sequence with the ambiguous character B.