[Inparanoid] InParanoid Digest, Vol 12, Issue 2

Milton Y. Nishiyama Jr. yutakajr at iq.usp.br
Tue Apr 29 13:12:28 CEST 2014


Hi Erik,

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 ?
I'm doing the analysis for grass plant species sugarcane,  sorghum, rice,
maize, panicum, estaria and brachypodium

Thank You

Milton
Em 29/04/2014 07:00, <inparanoid-at-sbc.su.se-request at lists.su.se> escreveu:

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> Today's Topics:
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>    1. orthologous gene assign (Jun Wang)
>    2. Re: orthologous gene assign (Erik Sonnhammer)
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> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 26 Apr 2014 18:10:52 +0000
> From: Jun Wang <junwang at unomaha.edu>
> To: "inparanoid at sbc.su.se" <inparanoid at sbc.su.se>
> Subject: [Inparanoid] orthologous gene assign
> Message-ID:
>         <
> eb107523f4624a4680019ec725b878c7 at BLUPR07MB849.namprd07.prod.outlook.com>
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> Content-Type: text/plain; charset="us-ascii"
>
> Hi,
> 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!
>
> Bests,
>
> Jun Wang
> University of Nebraska at Omaha
>
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> Message: 2
> Date: Mon, 28 Apr 2014 17:15:52 +0200
> From: Erik Sonnhammer <erik.sonnhammer at scilifelab.se>
> To: Jun Wang <junwang at unomaha.edu>,     "inparanoid at sbc.su.se"
>         <inparanoid at sbc.su.se>
> Subject: Re: [Inparanoid] orthologous gene assign
> Message-ID: <535E70A8.1040901 at scilifelab.se>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>
> Hi Jun,
>
> If the 4 species are "evolutionarily equidistant" from each other, then
> you can try to use MultiParanoid, http://multiparanoid.sbc.su.se/
>
> Also Hieranoid http://hieranoid.sbc.su.se/ may work, but we acknowledge
> that Hieranoid has some issues with accuracy at the moment.
>
> Bests
> Erik Sonnhammer
>
> On 04/26/2014 08:10 PM, Jun Wang wrote:
> >
> > Hi,
> >
> > 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!
> >
> > Bests,
> >
> > Jun Wang
> >
> > University of Nebraska at Omaha
> >
> >
> >
> > _______________________________________________
> > InParanoid mailing list
> > InParanoid at lists.su.se
> > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>
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> End of InParanoid Digest, Vol 12, Issue 2
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