MATLAB: How to execute smith waterman algorithm in matlab

smith waterman algorithm

I want to get an optimal sequence for given set of sequences. So, I am using Smith Water-man algorithm. How to execute that algorithm in Matlab?

Best Answer

http://www.mathworks.com/help/bioinfo/ref/swalign.html

See also http://www.mathworks.com/matlabcentral/fileexchange/45831-matlab-audio-analysis-library/content/library/smithWaterman.m if you want code for the algorithm itself.

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: Take input and use it in a function

Ahmad - please clarify what you mean by it doesn't seem to work. Are you observing an error or are you not getting the correct/desired results?

If I look at the documentation for getgenpept, one of the examples is

 Seq = getgenpept('AAA59174')

and it produces some result. You have even shown that something like

 human = getgenpept('AAA69808','SequenceOnly',true);
 chicken = getgenpept('NP_989750','SequenceOnly',true);

works too. So what is different between the above two statements and your code that gets the input from the user? Note what you are doing

 protein1=input('NCBI accession number  of the first protein: ', 's');
 protein2=input('NCBI accession number  of the second protein: ', 's');

protein1 and protein2 are variables of data type char (so are string variables). With your input example this means that

 protein1 == 'AAA69808'
 protein2 == 'NP_989750'

Now since these are string variables and the first input to the getgenpept is a string variable, there is no need to wrap these variables in quotes like

 seq1 = getgenpept('protein1','SequenceOnly',true);
 seq2 = getgenpept('protein2','SequenceOnly',true);

because if you do, then what you are really passing this function are strings representing the variable name of protein1 or protein2 and not the value of the variable.

Remove the single quotes and change these two lines to

 seq1 = getgenpept(protein1,'SequenceOnly',true);
 seq2 = getgenpept(protein2,'SequenceOnly',true);

Best Answer

Related Solutions

MATLAB: Does the function NT2AA translate the nucleotide sequence incorrectly

MATLAB: Take input and use it in a function

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