Hi,

maybe the following page can help in learning to read this kind of plot and your plot in particular: http://www.code10.info/index.php%3Foption%3Dcom_content%26view%3Darticle%26id%3D64:inroduction-to-dot-plots%26catid%3D52:cat_coding_algorithms_dot-plots%26Itemid%3D76, especially the section "Interpreting dot plots".

More generally, this kind of plot is called a "dot plot"; a "mummer plot" is basically a "dot plot" generated using the MUMMER alignment software, and there is other software which can be used to generate this kind of information/plot.

It seems to me that your query sequence starts somewhere in the middle of your target (base 3000000). Hence, it seems to me that the "start" coordinate of your query is wrong/different, which may be due to a missing/unsuccessful circularization attempt - based on the sequence lengths, I assume these are bacterial genomes.

Given similar start coordinates, I would expect your plot to look much more "diagonal", i.e., starting in the top left and running to the lower right with few off-diagonal elements, which is a good sign. Some breaks in the diagonal exist which are indicative of differences between the two sequences which is not unexpected.

I could suggest you two additional tools/approaches for the pairwise comparison of sequences: Circoletto @ http://tools.bat.infspire.org/circoletto/ and ANI calculator @ http://enve-omics.ce.gatech.edu/ani/.

Hope this helps.

Best,

Cedric

P.S. If you find an answer helpful, please consider up-voting it.

Hello Cedric, Thank you so much for the response. As you guessed they are bacterial genomes. I used the software which was provided by the sequencing company to create the Mummer plot . Thank you for the link which explains the dot plot. It really helps. I will go through the tools which you suggested to get a better picture of the similarity between the two genomes.

Best regards,

Bindu

Thank you so much for your input Lisandra. Really appreciate it. 

I will go through the programs which you suggested.

Thanks once again

Have a good one

Bindu