From hickt at smail.uni-koeln.de  Tue Jun  7 11:32:53 2016
From: hickt at smail.uni-koeln.de (Timon Hick)
Date: Tue, 7 Jun 2016 11:32:53 +0200
Subject: [Inparanoid] Missing Orthologs
Message-ID: <575694C5.7000708@smail.uni-koeln.de>

Dear InParanoid-Mailinglist,

I am currently working on a project, using inparanoid as orthology 
inference method. It is a human-centric project, so I retrieved all 
orthologs of human proteins available on the server and ran inparanoid 
against several other species.

We now found some missing orthologs and are wondering why they were not 
found.

As an example, you can have a look at the human protein BDP1 (Uniprot: 
A6H8Y1). There is neither an ortholog in the online-available data, nor 
in the results of my local runs.
When you perform a simple blast, you see BDP1 is present in mouse and 
yeast, for example.

Why are these proteins not found as orthologs?

There are 270 additional human proteins, for which orthologs were 
expected, but not found. If necessary, I could deliver those.

I would appreciate any ideas or help and thank you in advance for your 
answers.

Best wishes,

Timon

From hendrik.petersen at cos.uni-heidelberg.de  Fri Jun 24 10:29:41 2016
From: hendrik.petersen at cos.uni-heidelberg.de (Hendrik Petersen)
Date: Fri, 24 Jun 2016 10:29:41 +0200
Subject: [Inparanoid] broken download link
Message-ID: <20160624102941.jks542376sggwcs4@wwwmail.urz.uni-heidelberg.de>

Hey,

i tried to download the stand alone inparanoid software from the  
following link:

http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid

the website was not found.

is this only a temporary error? how can i get the software?

thanks,

Hendrik






From erik.sonnhammer at scilifelab.se  Mon Jun 27 12:12:23 2016
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Mon, 27 Jun 2016 12:12:23 +0200
Subject: [Inparanoid] broken download link
In-Reply-To: <20160624102941.jks542376sggwcs4@wwwmail.urz.uni-heidelberg.de>
References: <20160624102941.jks542376sggwcs4@wwwmail.urz.uni-heidelberg.de>
Message-ID: <5770FC07.6060102@scilifelab.se>

Sorry about that. Should be fixed now.

/Erik

On 06/24/2016 10:29 AM, Hendrik Petersen wrote:
> Hey,
>
> i tried to download the stand alone inparanoid software from the 
> following link:
>
> http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid
>
> the website was not found.
>
> is this only a temporary error? how can i get the software?
>
> thanks,
>
> Hendrik
>
>
>
>
>
> _______________________________________________
> InParanoid-at-sbc.su.se mailing list
> InParanoid-at-sbc.su.se at lists.su.se
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