[Inparanoid] InParanoid of 1 protein

[Erik Sonnhammer]

Dear Andrzej,

I'm afraid there is no facility in InParanoid to do that.

/Erik

On 10/02/2015 04:01 PM, Andrzej Zielezinski wrote:
> Dear Professor Sonnhammer,
>
> thank you for a quick reply. I'm aware that searching for orthologs 
> using the Reciprocal Best BLAST approach requires complete proteomes. 
> However, I don't have to BLAST all proteins in a proteome when I'm 
> interested only in one protein. I can BLAST a protein of interest 
> against a subject's complete proteome, then take a best hit and BLAST 
> it the other way against query's complete proteome. I was wondering 
> whether InParanoid can be used this way? For example, Reciprocal 
> Smallest Distance (RSD) approach lets users to find orthologs for 
> specific sequences in the query genome.
>
> Kindest regards,
> Andrzej ZIelezinski
>
>
> Andrzej Zielezinski, PhD
> Department of Computational Biology
> www: http://www.combio.pl
>
> On Fri, Oct 2, 2015 at 3:19 PM, Erik Sonnhammer 
> <erik.sonnhammer at scilifelab.se <mailto:erik.sonnhammer at scilifelab.se>> 
> wrote:
>
>     Hi, never use a subset - you need to use the complete proteomes
>     for the orthology assignments to be valid.
>
>     /Erik
>
>     On 02 Oct 2015, at 13:44, Andrzej Zielezinski <andrzejz at amu.edu.pl
>     <mailto:andrzejz at amu.edu.pl>> wrote:
>
>>     Dear Professor Sonnhammer,
>>
>>     thank you for sharing the standalone version of InParanoid.
>>
>>     I have a question regarding searching options in your software.
>>     Is it possible to search for orthologs/inparalogs only for
>>     specific sequences in the query genome. I would like to avoid a
>>     step where InParanoid calculates all-versus-all BLASTs of all
>>     proteins from query and subject genomes.
>>
>>     I would very much appreciate any guidance or advice you could
>>     provide on this matter.
>>
>>     Best regards,
>>     Andrzej ZIelezinski
>>
>>     ------------
>>     Andrzej Zielezinski, PhD
>>     Department of Computational Biology
>>     www: http://www.combio.pl
>>
>

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