dotplot for multifasta files

Question

[agata88]

Hi all!

I need to compare aligned genomes and visualize it with dotplot. I have used Gepard and D-Genies but I don't see the possibility to add clusters IDs into the chart. Also, cause of the large alignment file it is almost impossible to add this information by myself in graphic program. I was looking for some kind of solution in R? Is there a package where I can do similar plots to those generated by Gepard?

Many thanks for any suggestions,

Best, Agata

Answer 1

[JC]

https://rdrr.io/cran/seqinr/man/dotPlot.html

[agata88]

Thanks, I've tried it before. Well it is not for multiple sequence alignments but to compare between two sequences. Or maybe I don't understand it well.

[GenoMax]

Dot plots (LINK) are meant to be used with two sequences at a time. Are you looking to visualize multiple genomes? Perhaps something like mauve may be a better option.

[agata88]

Well, Gepard and D-genies are doing the work but charts output are illegible. What I need is to add clusters IDs into the charts like here: https://www.researchgate.net/figure/Cluster-relationships-are-evident-in-Gepard-dotplot-alignments-using-whole-genome_fig1_239946364

I thought that it will be possible to do with those programs but I didn't find an options. Adding info in graphic program is also very hard, cause my alignment is really large. I assumed that there must be some equivalent solution in R. R can produce such a great plots with proper custom labels etc. Unfortunately it has to be dotplot. To be honest I am really stuck in here.