Bioinformatics Toolbox

aa2nt

Convert an amino acid sequence to a nucleotide sequence

Syntax

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

Arguments

`SeqAA`	Amino acid sequence. Enter a character string or a vector of integers from the table . Examples: `'ARN'` or `[1 2 3]`
`GeneticCode`	Property to select a genetic code. Enter a code number or code name from the table Genetic Code below. If you use a code name, you can truncate the name to the first two characters of the name.
`Alphabet`	Property to select a nucleotide alphabet. Enter either `'DNA'` or `'RNA'`. The default value is `'DNA'`, which uses the symbols `A`, `C`, `T`, `G`. The value `'RNA'` uses the symbols `A`, `C`, `U`, `G`.

Genetic Code

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

Description

SeqNT = aa2nt(SeqAA, 'PropertyName', PropertyValue...) converts an amino acid sequence (SeqAA) to a nucleotide sequence (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 more then one possible nucleotide codon, this function selects randomly 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.

aa2nt(..., 'GeneticCode', GeneticCodeValue) selects a genetic code (GeneticCodeValue) to use when converting an amino acid sequence (SeqAA) to a nucleotide sequence (SeqNT).

aa2nt(..., 'Alphabet' AlphabetValue) selects a nucleotide alphabet (AlphabetValue).

Standard Genetic Code

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

Examples

Convert a amino acid sequence to a nucleotide sequence using the standard genetic code.

aa2nt('MATLAB')

Warning: The sequence contains ambiguous characters.
ans =
ATGGCAACCCTGGCGAAT

Use the Vertebrate Mitochondrial genetic code.

aa2nt('MATLAP', 'GeneticCode', 2)

ans =
ATGGCAACTCTAGCGCCT

Use the genetic code for the Echinoderm Mitochondrial RNA alphabet.

aa2nt('MATLAB','GeneticCode','ec','Alphabet','RNA')

Warning: The sequence contains ambiguous characters.
ans =
AUGGCUACAUUGGCUGAU

Convert a sequence with the ambiguous amino acid characters B.

aa2nt('abcd')

Warning: The sequence contains ambiguous characters.
ans =
GCCACATGCGAC

aa2nt

Syntax

Arguments

Description

Examples

See Also