Question: Mummer And Alignment Of Complete Genomes
2
gravatar for Ma
7.9 years ago by
Ma140
Ma140 wrote:

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

genome alignment • 2.7k views
ADD COMMENTlink modified 5.0 years ago by Biostar ♦♦ 20 • written 7.9 years ago by Ma140
1
gravatar for Damian Kao
7.9 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

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

ADD COMMENTlink modified 28 days ago by RamRS24k • written 7.9 years ago by Damian Kao15k
1
gravatar for ALchEmiXt
7.9 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

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).

ADD COMMENTlink written 7.9 years ago by ALchEmiXt1.9k
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