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<div class="moz-cite-prefix">Dear Andrzej,<br>
<br>
I'm afraid there is no facility in InParanoid to do that.<br>
<br>
/Erik<br>
<br>
On 10/02/2015 04:01 PM, Andrzej Zielezinski wrote:<br>
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<div>Dear Professor Sonnhammer, </div>
<div><br>
</div>
<div>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.</div>
<div><br>
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<div>Kindest regards,</div>
<div>Andrzej ZIelezinski</div>
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Andrzej Zielezinski, PhD
<div>Department of Computational Biology<br>
www: <a moz-do-not-send="true"
href="http://www.combio.pl" target="_blank">http://www.combio.pl</a></div>
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<div class="gmail_quote">On Fri, Oct 2, 2015 at 3:19 PM, Erik
Sonnhammer <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:erik.sonnhammer@scilifelab.se"
target="_blank">erik.sonnhammer@scilifelab.se</a>></span>
wrote:<br>
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.8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hi, never use a subset - you need to use the complete
proteomes for the orthology assignments to be valid.<span
class="HOEnZb"><font color="#888888"><br>
<br>
/Erik</font></span></div>
<div>
<div class="h5">
<div><br>
On 02 Oct 2015, at 13:44, Andrzej Zielezinski <<a
moz-do-not-send="true"
href="mailto:andrzejz@amu.edu.pl" target="_blank"><a class="moz-txt-link-abbreviated" href="mailto:andrzejz@amu.edu.pl">andrzejz@amu.edu.pl</a></a>>
wrote:<br>
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<div dir="ltr">Dear Professor Sonnhammer,
<div><br>
</div>
<div>thank you for sharing the standalone
version of InParanoid.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I would very much appreciate any guidance
or advice you could provide on this matter.<br>
</div>
<div><br>
</div>
<div>Best regards,</div>
<div>Andrzej ZIelezinski<br clear="all">
<div>
<div>
<div dir="ltr">
<div>
<div dir="ltr"><br>
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<div dir="ltr">------------<br>
Andrzej Zielezinski, PhD
<div>Department of Computational
Biology<br>
www: <a moz-do-not-send="true"
href="http://www.combio.pl"
target="_blank">http://www.combio.pl</a></div>
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