[Inparanoid] confidence value cutoff

Erik Sonnhammer erik.sonnhammer at scilifelab.se
Mon Sep 28 18:46:12 CEST 2015


Hi,

0.05 is "optimised for coverage". We have not actually done any proper 
optimisation of it, but we know that the false positive rate is low at 
this value, so one could even try to lower it.  But if you only want the 
very strongest orthologs then you can increase it.  On 
http://orthology.benchmarkservice.org we use default cutoff and 1.0.  
The main effect is that 1.0 gives much lower coverage.  Sometimes 1.0 
has better accuracy but sometimes not.  So unless you are particularly 
interested in 1-1 orthologs I recommend leaving it at 0.05.

Erik Sonnhammer

On 2015-09-28 16:42, Pengcheng Yang wrote:
> Hi Inparanoid developers,
>
> I am using Inparanoid to cluster proteins into groups to identify 
> ortholog genes. However, I have a questions about the confidence value 
> cutoff. Is it too low, default 0.05 to increase the false positive? 
> What is the optimized value you recommend?
>
> Thank you and best wishes,
>



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