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<div class="moz-cite-prefix">Hi,<br>
<br>
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?<br>
<br>
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)?<br>
<br>
/Erik<br>
<br>
On 09/29/2015 04:59 PM, Arjun Subedi wrote:<br>
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<blockquote
cite="mid:CA+LKX979YGAWZzVSdCc2JTt+MpNEwTjO=nvkYS_HHcCOy=VQiQ@mail.gmail.com"
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<div>Dear inparanoid developers,<br>
<br>
</div>
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?<br>
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<br>
</div>
Thank you<br>
<br>
</div>
Arjun Subedi<br>
</div>
<br>
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