<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">inparanoid-at-sbc.su.se-request@lists.su.se</a>> escreveu:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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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>
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Message: 1<br>
Date: Sat, 26 Apr 2014 18:10:52 +0000<br>
From: Jun Wang <<a href="mailto:junwang@unomaha.edu">junwang@unomaha.edu</a>><br>
To: "<a href="mailto:inparanoid@sbc.su.se">inparanoid@sbc.su.se</a>" <<a href="mailto:inparanoid@sbc.su.se">inparanoid@sbc.su.se</a>><br>
Subject: [Inparanoid] orthologous gene assign<br>
Message-ID:<br>
<<a href="mailto:eb107523f4624a4680019ec725b878c7@BLUPR07MB849.namprd07.prod.outlook.com">eb107523f4624a4680019ec725b878c7@BLUPR07MB849.namprd07.prod.outlook.com</a>><br>
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<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">erik.sonnhammer@scilifelab.se</a>><br>
To: Jun Wang <<a href="mailto:junwang@unomaha.edu">junwang@unomaha.edu</a>>, "<a href="mailto:inparanoid@sbc.su.se">inparanoid@sbc.su.se</a>"<br>
<<a href="mailto:inparanoid@sbc.su.se">inparanoid@sbc.su.se</a>><br>
Subject: Re: [Inparanoid] orthologous gene assign<br>
Message-ID: <<a href="mailto:535E70A8.1040901@scilifelab.se">535E70A8.1040901@scilifelab.se</a>><br>
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<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>
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