| Bioinformatics Toolbox | |
Convert nucleotide sequence to amino acid sequence
SeqAA = nt2aa(SeqNT, 'PropertyName', PropertyValue) nt2aa(..., 'Frame', FrameValue) nt2aa(..., 'GeneticCode', GeneticCodeValue) nt2aa(..., 'AlternativeStartCodons', AlternativeValue)
SeqNT | DNA nucleotide sequence. Enter a character string with only the characters A, T, C, and G. You cannot use the character U, ambiguous characters, or a hyphen. You can also enter a structure with the field Sequence. |
FrameValue | Property to select a frame. Enter 1, 2, 3, or 'ALL'. The default value is 1. |
GeneticCodeValue | Property to select a genetic code. Enter a code number or code name from the table Genetic Code. If you use a code name, you can truncate the name to the first two characters of the name. |
AlternativeValue | Property to control the use of alternative codons. Enter either true or false. The default value is true. |
Genetic Code
| Code Number | Code Name |
|---|---|
1 | Standard |
2 | Vertebrate Mitochondrial |
3 | Yeast Mitochondrial |
4 | Mold, Protozoan, and 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 |
SeqAA = nt2aa(SeqNT, 'PropertyName', PropertyValue) converts a nucleotide sequence to an amino acid sequence using the standard genetic code.
nt2aa(..., 'Frame', FrameValue) converts a nucleotide sequence for a specific reading frame to an amino acid sequence. If FrameValue equals 'ALL', then the three reading frames are converted and the output is a 3-by-1 cell array.
nt2aa(..., 'GeneticCode', GeneticCodeValue) converts a nucleotide sequence to an amino acid sequence using a specific genetic code.
nt2aa(..., 'AlternativeStartCodons', AlternativeValue) controls the use of alternative start codons. By default, AlternativeStartCodons is set to true, and if the first codon of a sequence corresponds to a known alternative start codon, the codon is translated to methionine.
If this option is set to false, then alternative start codons at the start of a sequence are translated to their corresponding amino acids for the genetic code that you use, which might not necessarily be methionine. For example, in the human mitochondrial genetic code, AUA and AUU are known to be alternative start codons.
For more details of alternative start codons, see
www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1
Convert the gene ND1 on the human mitochondria genome.
mitochondria = getgenbank('NC_001807','SequenceOnly',true)
gene = mitochondria (3308;4264)
protein1 = nt2aa(gene,'GeneticCode', 2)
protein2 = getgenpept('NP_536843',SequenceOnly',true)
Convert the gene ND2 on the human mitochondria genome. In this case, the first codon is att, which is converted to M, while the following att codons are converted to I. If you set 'AlternativeStartCodons' to false, then the first codon att is converted to I.
mitochondria = getgenbank('NC_001807','SequenceOnly',true)
gene = mitochondria (3371:4264)
protein1 = nt2aa(gene,'GeneticCcode',2)
protein2 = getgenpept('NP_536844', 'SequenceOnly',true)
Bioinformatics Toolbox functions aa2nt, baselookup, geneticcode, revgeneticcode
| | nmercount | nt2int | |
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