Are you using the MATLAB Bioinformatics package in particular, or are you writing your own in-house bioinformatic scripts for MATLAB?

I follow non of these procedure. I wanted to know how can I write codes and program to align sequences. I had 1200 sequence. I wanted to align them with each other. so I have to construct a 1200*1200 matrix. but I don't know how.

If you are not using any particular MATLAB component, then it might be much easier to run CLUSTALX and obtain the matrix without any coding at all. See http://www.embl.de/~seqanal/courses/commonCourseContent/usingClustalx.html#Obtaining_a_matrix_of_pairwise for details. Also running pairwise blastn/blastp on all pairs from a script may be a better option.

MATLAB is not designed to loop over a matrix, rather to perform operators on the entire matrix (without rigid constraints of sequence). You will find MATLAB to be quite inefficient when iterating over every element. I highly recommend you use arrayfun (http://www.mathworks.com/help/techdoc/ref/arrayfun.html) instead.

Hello Jamali,

It is very easy to write matlab code in few lines by using a loop for sequence alignment.

Thanks

Dear Mohammad, how? is it possible to send me that code?

@ali Send on some dummy data its simple todo it with loop or even without it.