MATLAB: Does the function NT2AA translate the nucleotide sequence incorrectly

Bioinformatics Toolbox

When I execute the command

nt2aa('ctg')

the resulting translation is 'M', however, the nucleotide sequence 'ctg' should map to the amino acid leucine ('L') in the standard genetic code.

Best Answer

The reason that 'CTG' at the beginning of a sequence results in the translation 'M' is that 'CTG' is an alternative start sequence in the standard genetic code (<http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c>). You may have observed that executing the command

     nt2aa('ctgctg')

results in the amino acid sequence

ML

The value of the 'AlternativeStartCodons' input parameter is used to control the use of alternative start codons by the NT2AA function. By default, 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 alternatives start codons at the start of a sequence are translated to their corresponding amino acids for the code that is being used.

To ignore alternative start codons when converting your nucleotide sequence to an amino acid sequence, please execute the following command:

     nt2aa('ctg', 'AlternativeStartCodons', false)

In this case, the resulting translation is 'L', as you had expected.

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MATLAB: Function Error / If and elseif statement help

As a replacement for what you have done here, I would suggest using ismember to find the triples that form valid codes. You can even use it to keep track of every marked position so you can see if you forgot to implement any triples.

amino_acid_chain = cellstr(reshape(neucleotide_string,3,[])');
L=false(size(amino_acid_chain));%keep track of replaced codes
library={{'E','GAA','GAG'};...
    {'W','UGG'}};%etc
for n=1:numel(library)
    triplet=library{n}(2:end);%select the triplet(s) from the library (e.g. {'GAA','GAG'})
    letter=library{n}(1);%select the corresponding amino acid letter (e.g. 'E')
    L_current_code=ismember(amino_acid_chain,triplet);%find all positions where the amino acid occurs
    amino_acid_chain(L_current_code)=letter;%replace by the letter code
    L=L | L_current_code;%mark as replaced
end
if any(~L)%shouldn't happen
    error('some code was not implemented correctly')
end

MATLAB: Do I get an error when I try to allign two sequences using LOCALALIGN function in Bioinformatics Toolbox 3.4 (R2009b)

The error you see is due to the fact that you are trying to align 2 sequences of different types. Sequence 'a' is a nucleotide sequence, and sequence 'b' is a amino acid sequence.

Best Answer

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MATLAB: Function Error / If and elseif statement help

MATLAB: Do I get an error when I try to allign two sequences using LOCALALIGN function in Bioinformatics Toolbox 3.4 (R2009b)

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