Question: What is the minimum percentage of identity (blastp) to predict the orthologous genes in different species?
gravatar for Dineshkumar K
7 days ago by
Kasaragod, Kerala, India
Dineshkumar K40 wrote:

I would like to predict the core genes/orthologous genes from different species of viruses. I have used roary to do the same, in which I could get least number of core genes while I set the minimum percentage identity of blastp is 30 to 40 (-i 30-40). Because, when I set the percentage of identity above 40 I could not get any core genes. Please some one clarify, is it the right way to do the analysis.

ADD COMMENTlink written 7 days ago by Dineshkumar K40

It sounds like you are trying to do core genome analysis among more distantly related bacteria. roary is only appropriate to approximately within genus comparisons (see their documentation).

A blastp identity of 30% is basically nothing. I would be seriously worried if you aren't getting any core genes with an identity over 40%. A typical value for roary would be 90-95% depending on how strict you want to be.

ADD REPLYlink written 7 days ago by Joe18k

@Joe Thank you for your valuable information and making me to aware the facts. I will not proceed the analysis with this low percentage of identity value.

ADD REPLYlink written 7 days ago by Dineshkumar K40
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