MATLAB: Why nucleotides is more than 4

nucleotides

hi as I know the no. of nucleotides is 4 letters. why in matlab consider it 17 letters as in table here:

http://www.mathworks.com/help/toolbox/bioinfo/ref/int2nt.html

thanks

Best Answer

The table there looks pretty straight-forward to me: http://www.mathworks.com/help/toolbox/bioinfo/ref/int2nt.html#bp_rekb-1 . It has codes for situations in which particular sets of nucleotides are known to be present or known to be absent.

Besides, the number of known nucleotides is not 4: it is currently 8. The 7th and 8th were announced in July 2011, with the 5th and 6th having been announced in April 2005.

Related Solutions

MATLAB: Does the function NT2AA translate the nucleotide sequence incorrectly

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.

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

Related Solutions

MATLAB: Does the function NT2AA translate the nucleotide sequence incorrectly

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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