nucmer and promer plots generated via mummerplot look identical?

Question

[Jennifer]

Hi,

I am trying to align two sequences with mummer. The sequences are fairly dissimilar, so I wanted to look at both nucmer and promer results. However, the plots generated via mummerplot look nearly identical. The reference and query fastas. Is there some sort error here? Additionally, I am not sure how to interpret these results.

Nucmer Plot:

Promer Plot:

I used the following to generate the promer mummerplot:

promer --prefix=promer  Ref.fasta Query.fasta
delta-filter -q -r promer.delta > promer.filter
mummerplot promer.filter -R Ref.fasta -Q Query.fasta --png

and this is for the nucmer mummerplot:

nucmer --maxgap=500 --mincluster=100 --prefix=nucmer  Ref.fasta Query.fasta
delta-filter -q -r nucmer.delta > nucmer.filter
mummerplot nucmer.filter -R Ref.fasta -Q Query.fasta --png

Does anyone know what is going wrong here? Thanks!

Answer 1

[Istvan Albert]

Nothing is wrong with the plots, I would caution against assuming something must be wrong just because you don't quite understand what it shows. It generates the wrong mental state and approach to solving the problem.

In this case, you should learn about dotplots and what they show, then the image would make more sense.

That being said, let's analyze the situation. The dot plots ought to be similar, right? After all, you align the same sequences first in nucleotide and then in peptide space. It would be a much bigger concern if the alignments were wildly different.

Then just as expected, the protein alignments show much longer sections of similarity than the nucleotide plots. The distance between two dots is the region of similarity. Note how many more dots the nucleotide-based alignments have. So it all behaves as expected. Protein alignments find longer regions of similarity.

Google the concept "dot plot alignment" and read up on what dotplots show.

As with everything that has to do with alignments, dot plots can be very simple yet may also show surprisingly complex patterns that are not so easy to explain fully.