Question: Is it possible to carry-out pan-genome analysis of interspecies bacterial genome?
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gravatar for Kumar
2.0 years ago by
Kumar40
India
Kumar40 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 2.0 years ago by Joe18k • written 2.0 years ago by Kumar40
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gravatar for Joe
2.0 years ago by
Joe18k
United Kingdom
Joe18k 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 2.0 years ago by Joe18k

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 23 months ago • written 23 months ago by Kumar40
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