aa2nt

Convert amino acid sequence to nucleotide sequence

Syntax

ntSeq = aa2nt(aaSeq)

ntSeq = aa2nt(aaSeq,Name=Value)

Description

ntSeq = aa2nt(aaSeq) converts an amino acid sequence aaSeq to a nucleotide sequence ntSeq using the standard genetic code.

ntSeq = aa2nt(aaSeq,Name=Value) uses additional options specified by one or more name-value arguments. For example, ntSeq = aa2nt(aaSeq,GeneticCode=2) uses the vertebrate mitochondrial genetic code.

Examples

Convert an amino acid sequence to a nucleotide sequence

Create an amino acid sequence.

rng('default') % For reproducibility
seq = randseq(20,Alphabet="amino")

seq = 
'TYNYMRQLVVDVVITNHYSV'

Convert it to a nucleotide sequence using the standard genetic code.

aa2nt(seq)

ans = 
'ACATATAACTACATGAGACAGCTTGTAGTTGACGTTGTCATTACTAACCACTATAGCGTT'

Convert it using the vertebrate mitochondrial genetic code.

aa2nt(seq,GeneticCode=2)

ans = 
'ACCTATAACTACATACGCCAACTCGTAGTGGATGTAGTAATTACTAATCACTATTCGGTT'

Convert using the Echinoderm Mitochondrial genetic code and the RNA alphabet.

aa2nt(seq,GeneticCode="ec",Alphabet="RNA")

ans = 
'ACGUAUAACUACAUGCGGCAGUUAGUUGUCGACGUCGUGAUUACGAACCAUUAUAGUGUC'

Input Arguments

aaSeq — Amino acid sequence

character vector | string | row vector of positive integers | structure

Amino acid sequence, specified as one of the following.

• Character vector or 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.

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.

Example: "TYNYMRQLVV"

Data Types: char | string

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Example: ntseq = aa2nt(seq,GeneticCode=2,Alphabet="RNA")

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

Example: ntseq = aa2nt(seq,'GeneticCode',"ec",'Alphabet',"RNA")

GeneticCode — Genetic code number or name

1 or "Standard" (default) | positive integer | character vector | string scalar

Genetic code number or name, specified as a positive integer, character vector, or string scalar. The following table has the list of genetic codes and their corresponding code names.

Genetic Code Number	Genetic 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

Tip

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

The amino acid to nucleotide codon mapping for the standard genetic code is shown next.

Amino Acid Name	Amino Acid Code	Nucleotide Codon
Alanine	A	GCT GCC GCA GCG
Arginine	R	CGT CGC CGA CGG AGA AGG
Asparagine	N	AAT 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† † indicates an alternative start codon for the standard genetic code as defined here. If you are using nt2aa, alternative start codons are converted to methionine (M) when one of these codons is the first codon of a sequence and AlternativeStartCodons is set to true.
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)	?	???

Data Types: double | char | string

Alphabet — Nucleotide alphabet

"DNA" (default) | "RNA"

Nucleotide alphabet, specified as "DNA" or "RNA". If "DNA", the function uses A, C, G, and T. If "RNA", the function uses A, C, G, and U.

Data Types: char | string

Output Arguments

ntSeq — Nucleotide sequence

character vector

Nucleotide sequence, returned as a character vector.

Version History

Introduced before R2006a