Bioinformatics Toolbox™

nt2aa - Convert nucleotide sequence to amino acid sequence

Syntax

SeqAA = nt2aa(SeqNT)

SeqAA = nt2aa(..., 'Frame', FrameValue, ...)
SeqAA = nt2aa(..., 'GeneticCode', GeneticCodeValue, ...)
SeqAA = nt2aa(..., 'AlternativeStartCodons', AlternativeStartCodonsValue, ...)

Arguments

Return Values

Description

SeqAA = nt2aa(SeqNT) converts a nucleotide sequence, specified by SeqNT, to an amino acid sequence, returned in SeqAA, using the standard genetic code.

SeqAA = nt2aa(SeqNT, ...'PropertyName', PropertyValue, ...) calls nt2aa 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:

SeqAA = nt2aa(..., 'Frame', FrameValue, ...) converts a nucleotide sequence for a specific reading frame to an amino acid sequence. Choices are 1, 2, 3, or 'all'. Default is 1. If FrameValue is 'all', then output SeqAA is a 3-by-1 cell array.

SeqAA = nt2aa(..., 'GeneticCode', GeneticCodeValue, ...) specifies a genetic code to use when converting a nucleotide sequence to an amino acid 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.

SeqAA = nt2aa(..., 'AlternativeStartCodons', AlternativeStartCodonsValue, ...) controls the translation of alternative start codons. By default, AlternativeStartCodonsValue is set to true, and if the first codon of a sequence is a known alternative start codon, the codon is translated to methionine.

If this option is set to false, then an alternative start codon at the start of a sequence is translated to its corresponding amino acid in the genetic code that you specify, 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 information about alternative start codons, see:

www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1

Genetic Code

Standard Genetic Code

Examples

Converting the ND1 Gene

1. Use the getgenbank function to retrieve the nucleotide sequence for the human mitochondrion from the GenBank database.

   mitochondria = getgenbank('NC_001807', 'SequenceOnly', true);
   

2. Extract the sequence for the ND1 gene from the nucleotide sequence.

   ND1gene = mitochondria (3308:4261);
   

3. Convert the ND1 gene on the human mitochondria genome to an amino acid sequence using the Vertebrate Mitochondrial genetic code.

   protein1 = nt2aa(ND1gene,'GeneticCode', 2);
   

4. Use the getgenpept function to retrieve the same amino acid sequence from the GenPept database.

   protein2 = getgenpept('NP_536843', 'SequenceOnly', true);
   

5. Use the isequal function to compare the two amino acid sequences.

   isequal (protein1, protein2)
   
   ans =
   
        1

Converting the ND2 Gene

1. Use the getgenbank function to retrieve the nucleotide sequence for the human mitochondrion from the GenBank database.

   mitochondria = getgenbank('NC_001807', 'SequenceOnly', true);
   

2. Extract the sequence for the ND2 gene from the nucleotide sequence.

   ND2gene = mitochondria (4471:5511);
   

3. Convert the ND2 gene on the human mitochondria genome to an amino acid sequence using the Vertebrate Mitochondrial genetic code.

   protein1 = nt2aa(ND2gene,'GeneticCode', 2);
   

   Note   In the ND2gene nucleotide sequence, the first codon is ATT, which is translated to M, while the subsequent ATT codons are translated to I. If you set 'AlternativeStartCodons' to false, then the first ATT codon is translated to I, the corresponding amino acid in the Vertebrate Mitochondrial genetic code.

4. Use the getgenpept function to retrieve the same amino acid sequence from the GenPept database.

   protein2 = getgenpept('NP_536844', 'SequenceOnly', true);
   

5. Use the isequal function to compare the two amino acid sequences.

   isequal (protein1, protein2)
   
   ans =
   
        1

See Also

Bioinformatics Toolbox functions: aa2nt, aminolookup, baselookup, codonbias, dnds, dndsml, geneticcode, revgeneticcode, seqtool

nmercount

nt2int