MATLAB: Does the Bioinformatics Toolbox support Selenocysteine

acidaminoaminolookupBioinformatics Toolboxmartixnwalginscoringselenocysteine

Type the following at MATLAB Command Prompt:
aminolookup('U')
The result is void.
When this result is used for alignment, I obtain the following error message:
 Error Messages (if any): nwalign ('yvu','yvu')
 ??? Error using ==> nwalign
 Both sequences must be either amino acids or nucleotides

Best Answer

This error occurs since the Bioinformatics Toolbox does not support the amino acid Selenocysteine with symbol 'U'. Hence NWALIGN fails.
The problem with alignment is that none of the standard scoring matrices for alignment include Selenocysteine. One possible workaround is to convert U to X (the symbol for 'any' amino acid) and then the alignment will not error out.
A code similar to the following can be used to avoid the error:
Seq1 =  'uarndcqeghilkumfpstwyv';
Seq2 =  'auurndcqeghilkmufpstwyv';
Seq1_X = strrep(Seq1,'u','x');
Seq2_X = strrep(Seq2,'u','x');
[score,alignment] = nwalign(Seq1_X,Seq2_X);
alignment = reshape(strrep(alignment(:)','X','U'),size(alignment));
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