<div dir="ltr">Hi Erik,<div><br></div><div>Thank You for your reply, that will be very important in my studies. If you get any news please let me know.</div><div><br></div><div>Best,</div><div><br></div><div>Milton</div></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Apr 29, 2014 at 9:06 AM, Erik Sonnhammer <span dir="ltr"><<a href="mailto:erik.sonnhammer@scilifelab.se" target="_blank">erik.sonnhammer@scilifelab.se</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div>Hi Milton,<br>
<br>
yes I think you need to worry about it. In the Hieranoid paper we
benchmarked with OrthoBench, believing this was a good test. But
after the paper came out we realised that it only measures
sensitivity and not specificity. We have recently done some
specificity tests and here Hieranoid performs significantly worse
than InParanoid, i.e. it has many more false positives.
Unfortunately nobody has worked on Hieranoid since the paper came
out so we have not resolved this yet, but a new graduate student
has just picked up the thread so we hope to be able to fix it
soonish. We still don't know what the problem is, so I can't give
any estimates of how long it may take.<br>
<br>
Yours<span class="HOEnZb"><font color="#888888"><br>
Erik Sonnhammer</font></span><div><div class="h5"><br>
<br>
On 04/29/2014 01:12 PM, Milton Y. Nishiyama Jr. wrote:<br>
</div></div></div><div><div class="h5">
<blockquote type="cite">
<p dir="ltr">Hi Erik,</p>
<p dir="ltr">I would like to know what kind of accuracy issue the
hieranoid has, because I'm using it over 6 species not exactly
equidistant and I would like to know if there something that I
would need to worry about it ?<br>
I'm doing the analysis for grass plant species sugarcane,
sorghum, rice, maize, panicum, estaria and brachypodium</p>
<p dir="ltr">Thank You<br>
</p>
<p dir="ltr">Milton<br>
</p>
<div class="gmail_quote">Em 29/04/2014 07:00, <<a href="mailto:inparanoid-at-sbc.su.se-request@lists.su.se" target="_blank">inparanoid-at-sbc.su.se-request@lists.su.se</a>>
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Today's Topics:<br>
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1. orthologous gene assign (Jun Wang)<br>
2. Re: orthologous gene assign (Erik Sonnhammer)<br>
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----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Sat, 26 Apr 2014 18:10:52 +0000<br>
From: Jun Wang <<a href="mailto:junwang@unomaha.edu" target="_blank">junwang@unomaha.edu</a>><br>
To: "<a href="mailto:inparanoid@sbc.su.se" target="_blank">inparanoid@sbc.su.se</a>"
<<a href="mailto:inparanoid@sbc.su.se" target="_blank">inparanoid@sbc.su.se</a>><br>
Subject: [Inparanoid] orthologous gene assign<br>
Message-ID:<br>
<<a href="mailto:eb107523f4624a4680019ec725b878c7@BLUPR07MB849.namprd07.prod.outlook.com" target="_blank">eb107523f4624a4680019ec725b878c7@BLUPR07MB849.namprd07.prod.outlook.com</a>><br>
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Content-Type: text/plain; charset="us-ascii"<br>
<br>
Hi,<br>
I am now dealing with the comparative genomic project, I want
to do orthologous analysis, so I use this inparanoid4.1
software, and it is good. While my problem is: I have more
than two species, for example, I have four species (A, B, C,
D), how can do it with inparanoid software in order to have
the orthologous gene among the four species. Should I do like
this (AB, AC, AD, BC, BD, CD)? And then extract the
orthologous gene name manually? Thank you very much, I really
appreciate it!<br>
<br>
Bests,<br>
<br>
Jun Wang<br>
University of Nebraska at Omaha<br>
<br>
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Message: 2<br>
Date: Mon, 28 Apr 2014 17:15:52 +0200<br>
From: Erik Sonnhammer <<a href="mailto:erik.sonnhammer@scilifelab.se" target="_blank">erik.sonnhammer@scilifelab.se</a>><br>
To: Jun Wang <<a href="mailto:junwang@unomaha.edu" target="_blank">junwang@unomaha.edu</a>>,
"<a href="mailto:inparanoid@sbc.su.se" target="_blank">inparanoid@sbc.su.se</a>"<br>
<<a href="mailto:inparanoid@sbc.su.se" target="_blank">inparanoid@sbc.su.se</a>><br>
Subject: Re: [Inparanoid] orthologous gene assign<br>
Message-ID: <<a href="mailto:535E70A8.1040901@scilifelab.se" target="_blank">535E70A8.1040901@scilifelab.se</a>><br>
Content-Type: text/plain; charset="iso-8859-1";
Format="flowed"<br>
<br>
Hi Jun,<br>
<br>
If the 4 species are "evolutionarily equidistant" from each
other, then<br>
you can try to use MultiParanoid, <a href="http://multiparanoid.sbc.su.se/" target="_blank">http://multiparanoid.sbc.su.se/</a><br>
<br>
Also Hieranoid <a href="http://hieranoid.sbc.su.se/" target="_blank">http://hieranoid.sbc.su.se/</a>
may work, but we acknowledge<br>
that Hieranoid has some issues with accuracy at the moment.<br>
<br>
Bests<br>
Erik Sonnhammer<br>
<br>
On 04/26/2014 08:10 PM, Jun Wang wrote:<br>
><br>
> Hi,<br>
><br>
> I am now dealing with the comparative genomic project, I
want to do<br>
> orthologous analysis, so I use this inparanoid4.1
software, and it is<br>
> good. While my problem is: I have more than two species,
for example,<br>
> I have four species (A, B, C, D), how can do it with
inparanoid<br>
> software in order to have the orthologous gene among the
four species.<br>
> Should I do like this (AB, AC, AD, BC, BD, CD)? And then
extract the<br>
> orthologous gene name manually? Thank you very much, I
really<br>
> appreciate it!<br>
><br>
> Bests,<br>
><br>
> Jun Wang<br>
><br>
> University of Nebraska at Omaha<br>
><br>
><br>
><br>
> _______________________________________________<br>
> InParanoid mailing list<br>
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End of InParanoid Digest, Vol 12, Issue 2<br>
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</blockquote>
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<fieldset></fieldset>
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<pre>_______________________________________________
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</blockquote>
<br>
</div></div></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br>=================================================<br> Milton Yutaka Nishiyama Jr. <br> PhD Student<br> Bioinformatics Group - IME/IQ - USP<br> Biochemistry Department, University of Sao Paulo<br>
<a href="http://sucest-fun.org/" target="_blank">http://sucest-fun.org/</a><br> Brazil<br>=================================================<br>
</div>