[Inparanoid] low number of orthologs

[Erik Sonnhammer]

Hi,

If you mean that you get 60 orthologs to S. cerevisiae then yes that is 
less than expected.  Are your 12000 protein sequences full-length?

You may have some technical problems with the sequence file that makes 
Blast choke, check for Blast errors.  How many homologs did you get (see 
inparanoid text output header)?

/Erik

On 09/29/2015 04:59 PM, Arjun Subedi wrote:
> Dear inparanoid developers,
>
> I am using inparanoid to derive orthologs for a newly sequenced 
> fungus. My organism consists 12000 protein sequence. When I run the 
> inparanoid with default settings against yeast (as protein B) it 
> yields only 60 orthologs, which I think is a very low number. Then I 
> splitted the sequence of both organism and took only half of the 
> sequences of each organism. Then I run a inparanoid, and it gives 
> higher no of othologs (214). Does it mean something wrong in my 
> sequence file or any other issues with bigger file?
>
> Thank you
>
> Arjun Subedi
>
>
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