Convert amino acid sequence to nucleotide sequence
SeqNT = aa2nt(SeqAA)
SeqNT =
aa2nt(SeqAA, ...'GeneticCode', GeneticCodeValue,
...)
SeqNT = aa2nt(SeqAA,
...'Alphabet' AlphabetValue, ...)
SeqAA | One of the following:
Examples: |
GeneticCodeValue | Integer, character vector, or string specifying a genetic code number or code name from
the table Genetic Code. Default is
Tip If you use a code name, you can truncate the name to the first two letters of the name. |
AlphabetValue | Character vector or string specifying a nucleotide alphabet. Choices are:
|
SeqNT | Nucleotide sequence specified by a character vector of letter codes. |
SeqNT = aa2nt(SeqAA)SeqAASeqNT,
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,
...)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:
specifies a genetic code to use when converting an amino acid sequence to a nucleotide
sequence. SeqNT =
aa2nt(SeqAA, ...'GeneticCode', GeneticCodeValue,
...)GeneticCodeValue can be an integer, character
vector, 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, ...)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 | 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 |
| 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) | ? | ??? |
aminolookup | baselookup | geneticcode | nt2aa | rand | revgeneticcode | seqviewer