Mummer And Alignment Of Complete Genomes

Question

[Ma]

Hi: I need to use Mummer for the alignment of two strainds of the complete genomes from Aspergillusfumigatus a239 and fgsca3, when I got the mummerplot the results seems scattered, I suppose that for this two type of genomes as being almost similar I should get almost a perfect diagonal in mummerplot? does anybody knows what parameters should I use in mummer for this type of alignments? also which option of mummer will be more exact? Thanks

Answer 1

[Damian Kao]

It could be due to repetitive/duplicated/rearranged regions. Maybe mgap will be of some use. You can read about mgap.

Answer 2

[ALchEmiXt]

You probably used nucmer for the alignment? If you try using promer (takes a significant longer time) it will usually elininate most of the noise/scatter (asmentioned coming from duplications/repeats and such). Result in most of our cases a more cleaner but highly similar plot (but on protein so its a different method/answer actually).