**20**wrote:

Hi All, I m quiet new to R Programming. My question may not be very wise, but would like to have some help as I explore more on R. Thanks in advance!

I have a matrix which was constructed based on comparing two sequences (say A and B) A="ATGCTAC" and B="ATCAGAT" and the matrix will be like M(1,1)=1,M(1,2)=1,M(1,3)=0. i.e., similar base positions with 1 and non-similar ones with 0. How can I construct a Dot Matrix plot?

Also if there is any code for Dot Matrix Alignment that uses window and stringency.

Anish