How to measure the similarity?

[Fad2012]

Hello All

I am dealing with a genome fragment of 2500 nucleotides from two serotypes of virus. Their genomes are 85% identical. I want to measure the similarity between them using a window of 10 nucleotides that moves, nucleotide after the other, from one side of the genome to the other. That is, first start with the similarity between the first 10 nucleotides, take the percentage similarity, then move one nucleotide and measure the similarity again between the 10 nucleotides, and then move the window one more nucleotide and measure the similarity…till the end of the fragment. Then plot them (x = location (number of nucleotide), Y= the percentage of similarity) , so the final graph will represent a fluctuating line.

I am looking for a tool or code that can carry out this job?

Many thanks

[GenoMax]

Dot plots (http://en.wikipedia.org/wiki/Dot_plo...informatics%29) is what you are looking for.


There are online implementations http://www.vivo.colostate.edu/molkit/dnadot/ and local programs (in fact this one appears to be for viral genomes http://sourceforge.net/projects/genomdiff/).

[Fad2012]

Thanks very much GenoMax