MATLAB: Alignment(3,:) in seqinsertgaps

bioinformatics

Hi guys. There's someone able to explain me why in seqinsertgaps for the alignment (al) I have to choose the first and the third line?i.e al(1,:)

al(3,:) What should be the general criterion? Thanks a lot

Best Answer

The alignment returned by nwalign is a 3xN character array showing the optimal alignment between the two input protein sequences. The first row is the first input sequence, the middle row shows alignment information, and the last shows the second sequence:

>> al(:,1:10)
ans =
  3×10 char array
    'QKQEIKMNPN'
    '      ||||'
    '------MNPN'

We then use seqinsertgaps to get the original nucleotide sequence, but with the gap information returned by the alignment, so the inputs are the first and third rows of the alignment character vector.

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: Does the score returned by NWALIGN not behave intuitively when I use the ambiguous symbols ‘W’ or ‘V’ in the Bioinformatics Toolbox 3.0 (R2007b)

The expections listed above are correct. However, the reason you are seeing a difference in the outputs is because by default the alignment functions assume the input sequences are aminoacids and therefore the alignments are scored with the BLOSUM50 matrix, if you change the alphabet to nucleotides the default scoring matrix is NUC44, this matrix accounts for scores between ambiguous nucleotide symbols appropriately. This is shown below:

 Score = nwalign('AACT','AACT','alpha','nt')
 >>Score =
     5.5463
 Score = nwalign('AGCT','AACT','alpha','nt')
 >>Score =
     3.0505
 Score = nwalign('AWCT','AACT','alpha','nt')
 >>Score =
     4.4371
 Score = nwalign('AVCT','AACT','alpha','nt')
 >>Score =
     3.8824

Best Answer

Related Solutions

MATLAB: Does the function NT2AA translate the nucleotide sequence incorrectly

MATLAB: Does the score returned by NWALIGN not behave intuitively when I use the ambiguous symbols ‘W’ or ‘V’ in the Bioinformatics Toolbox 3.0 (R2007b)

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