Question: Is it possible to carry-out pan-genome analysis of interspecies bacterial genome?
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gravatar for Dineshkumar K
6 months ago by
Kasaragod, Kerala, India
Dineshkumar K10 wrote:

I would like to carry-out pan-genome analysis of 3 different species genome, belongs to same genus. Most of the pan-genome analysis had been done intraspcies/same species genome. Therefore, is it a right way to carryout pan-genome analysis of interspecies/different species bacterial genome.

ADD COMMENTlink modified 6 months ago by jrj.healey13k • written 6 months ago by Dineshkumar K10
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gravatar for jrj.healey
6 months ago by
jrj.healey13k
United Kingdom
jrj.healey13k wrote:

You could take a look at any of: Roary, OrthoMCL, PanOCT, PanSeq, LS-BSR, FindMyFriends, PopPunk, MicroPan and PGAP.

I know Roary is only intended to be used with fairly closely related organisms, so take a look at the documentation for the others and there may be one more suited to distant comparisons (or you can use any of them and play with the various thresholds which seem reasonably given the relatedness (or lack thereof) of your organisms.

ADD COMMENTlink written 6 months ago by jrj.healey13k

Thank you healey, I would like to use BPGA (Bacterial Pan Genome Analysis tool) and as you suggested, I would play with various thresholds for the same.

ADD REPLYlink modified 5 months ago • written 5 months ago by Dineshkumar K10
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