Question: Whole genome alignments
0
gravatar for oussriradnane
5 weeks ago by
oussriradnane0 wrote:

hi I want to do a complete genome alignment of fungal isolates using the MUMmer software NUCmer and PROmer algorithms I want to determine the degree of overlap between genomes how can I do that??

alignment genome • 162 views
ADD COMMENTlink written 5 weeks ago by oussriradnane0

What do you mean by 'overlap'?

ADD REPLYlink written 5 weeks ago by jrj.healey12k

homology

ADD REPLYlink written 5 weeks ago by oussriradnane0

How many genomes have you got? if its more than about 4-5, alignment is not the right approach.

Please edit your post with much more information, it's hard to drag it out one word at a time to get to an answer.

ADD REPLYlink written 5 weeks ago by jrj.healey12k

I have 10 genomes , I want to make a comparative analysis of these genomes to determine the evolutionary relationship between the strains

ADD REPLYlink written 5 weeks ago by oussriradnane0
1

You cannot align that many genomes of that size. It simply won't work.

If you want to know similarity, you could use fastANI, or mash sketches. If you want to infer phylogenetic relationships though, you will probably be best off trying to define a core genome, and then using concatenated gene alignments.

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by jrj.healey12k

thank you

ADD REPLYlink written 5 weeks ago by oussriradnane0

my strains have 4 chromosomes, can I compare chrormosome by chromosome or gather all genes (concatenated) in a sequence and deduce it as a single genome

ADD REPLYlink written 5 weeks ago by oussriradnane0

You could probably do either, so long as your orthologue clustering is sufficiently reliable

ADD REPLYlink written 5 weeks ago by jrj.healey12k
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