[Inparanoid] confidence value cutoff
Pengcheng Yang
yangpc at biols.ac.cn
Tue Sep 29 01:51:19 CEST 2015
Hi Erik Sonnhammer,
Thank you for your reply.
One phenomenon is found that for the two organisms A and B with A-1 and
B-1, B-2 proteins, respectively. These three proteins clustered into one
ortholog group.
I found that the parsed blast results contain the hit records between
A-1 and B-1, B-1 and B-2, but not A-1 and B-2. However, this is possible
because blast_parser.pl set several criteria to filtering the alignment.
Ok, I will leave it at 0.05.
Thank you.
Pengcheng
On 2015/9/29 0:46, Erik Sonnhammer wrote:
> 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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