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Question: Is it possible to carry-out pan-genome analysis of interspecies bacterial genome?
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gravatar for Dineshkumar K
26 days ago by
Dineshkumar K • 0
Kasaragod, Kerala, India
Dineshkumar K • 0 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.
sequencing sequence next-gen gene genome • 74 views
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modified 26 days ago by jrj.healey ♦ 10k • written 26 days ago by Dineshkumar K • 0
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26 days ago by
jrj.healey ♦ 10k
United Kingdom
jrj.healey ♦ 10k 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 COMMENT • link written 26 days ago by jrj.healey ♦ 10k
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