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Is it possible to carry-out pan-genome analysis of interspecies bacterial genome?

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.

genome next-gen sequencing sequence gene
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updated by Joe Joe • written by Kumar Kumar

1 answer

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.

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written by Joe Joe

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.

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written by Kumar Kumar

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