[Inparanoid] InParanoid Digest, Vol 12, Issue 2
Erik Sonnhammer
erik.sonnhammer at scilifelab.se
Tue Apr 29 14:06:20 CEST 2014
Hi Milton,
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.
Yours
Erik Sonnhammer
On 04/29/2014 01:12 PM, Milton Y. Nishiyama Jr. wrote:
>
> 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
> <mailto:inparanoid-at-sbc.su.se-request at lists.su.se>> escreveu:
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> Today's Topics:
>
> 1. orthologous gene assign (Jun Wang)
> 2. Re: orthologous gene assign (Erik Sonnhammer)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 26 Apr 2014 18:10:52 +0000
> From: Jun Wang <junwang at unomaha.edu <mailto:junwang at unomaha.edu>>
> To: "inparanoid at sbc.su.se <mailto:inparanoid at sbc.su.se>"
> <inparanoid at sbc.su.se <mailto:inparanoid at sbc.su.se>>
> Subject: [Inparanoid] orthologous gene assign
> Message-ID:
>
> <eb107523f4624a4680019ec725b878c7 at BLUPR07MB849.namprd07.prod.outlook.com
> <mailto:eb107523f4624a4680019ec725b878c7 at BLUPR07MB849.namprd07.prod.outlook.com>>
>
> 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
> <mailto:erik.sonnhammer at scilifelab.se>>
> To: Jun Wang <junwang at unomaha.edu <mailto:junwang at unomaha.edu>>,
> "inparanoid at sbc.su.se <mailto:inparanoid at sbc.su.se>"
> <inparanoid at sbc.su.se <mailto:inparanoid at sbc.su.se>>
> Subject: Re: [Inparanoid] orthologous gene assign
> Message-ID: <535E70A8.1040901 at scilifelab.se
> <mailto: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 <mailto:InParanoid at lists.su.se>
> > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>
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