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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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How to choose right blastp minimum precent indentity and mcl inflation value? #551

Open AmayAgrawal opened 2 years ago

AmayAgrawal commented 2 years ago

This is more of a query instead of an issue. I am a bit confused about how to choose an optimum value of minimum percentage identity for blastp as well as the MCL inflation value?

I read in some of the posts here that the authors recommend to use > 90% identity for blastp, but I did not find anything related to this in either the paper or the supplementary material.

It would be highly appreciated if someone can give any suggestions about how to choose right value for blastp identity and mcl inflation value

hhj00123 commented 1 year ago

@AmayAgrawal
Hi, bro. Now, do you have a good idea？ When I use Roary, I found that genes with the same function are divided into different clusters. I think we should adjust identity for blastp as well as the MCL inflation value. But, I also don’t know which value is suitable？