From sammy.ich17 at gmail.com  Thu Oct  1 14:52:17 2015
From: sammy.ich17 at gmail.com (Sammy Desilva)
Date: Thu, 1 Oct 2015 14:52:17 +0200
Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid
In-Reply-To: <CAFqN6s6Q-Xe5_0R4Ru5Ch-DXKH+BLR+EeXF7R8N42_+FZrb2yw@mail.gmail.com>
References: <CAJXH_1ObFRxxcUSdpo--fLv8eXzhDQRbBvfb7zN4KBqEUhr3Xg@mail.gmail.com>
 <54201701.2050607@scilifelab.se>
 <CAJXH_1OEaf_nOduKihVNPT21BmPCfCCkehX8pLZZ8GHQOL+7tQ@mail.gmail.com>
 <CAPf=4Rf4vWPWiHAA9Pz=Np2i0d3bUspdtd1rX-AZMTsc8NJx_Q@mail.gmail.com>
 <CAJXH_1MWGaETkJBCtD+6_Sx5dwjQKx_1GBPZVw5ZkvbpAETHHg@mail.gmail.com>
 <CAFqN6s6Q-Xe5_0R4Ru5Ch-DXKH+BLR+EeXF7R8N42_+FZrb2yw@mail.gmail.com>
Message-ID: <CAJXH_1NuP=UKOQB2D8uThMwPGERRPoLuMEsD=CjL_m9W-on1RQ@mail.gmail.com>

Dear all,

So finally I canceled the computations. Can you please check the error log
file (attached) and let me know
what exactly is the problem?


*Thanks*
*Sammy*

On Tue, Sep 29, 2015 at 4:53 PM, Verena Haunschmid <veroamilbe at gmail.com>
wrote:

> Dear Sammy,
>
> I once did comparisons of several organisms and had the same problem as
>  you. To speed it up a little bit I precomputed the blast files since that
> is the most time consuming step as far as I remember.
>
> And if you do comparisons A-B, A-C, B-C, ... you would need to compute the
> blast output for A-A, B-B, C-C several times and that's half of the
> computation time for each pairwise comparison. Just compute all blast files
> for each organism with itself and uncomment those lines in the perl script.
> (might be that I still have these script, I will check later...)
>
> Best regards,
> Verena
>
>
>
> On Tue, Sep 29, 2015 at 4:46 PM Sammy Desilva <sammy.ich17 at gmail.com>
> wrote:
>
>> Dear all,
>>
>> I am again starting this thread here again. At that time I finally
>> shifted to normal PC instead of cluster. Now, I am analyzing 29 proteome
>> for orthology with multiparanoid. I used  the above script with sbatch seq
>> array in slurm but it  is still not finished in 15 days. Is there any
>> alternative way exist for doing this computations/
>>
>> Thnaks
>>
>> On Tue, Oct 7, 2014 at 1:39 PM, mateusz.kaduk at gmail.com <
>> mateusz.kaduk at gmail.com> wrote:
>>
>>> Dear Sammy,
>>>
>>> There is no script with inparanoid to automate pairwise runs, but I am
>>> using the following code to run all n(n-1)/2 pairwise comparisons without
>>> outgroup, it's just few lines of code, but maybe you will find it useful.
>>>
>>> #!/usr/bin/perl
>>> use strict;
>>> use warnings;
>>>
>>> # Here is the list of fasta files in the same directory as inparanoid.pl
>>> my @species = ("c_albicans-2011-04i.fa",
>>>                "c_neoformans-2011-04i.fa",
>>>                "s_cerevisiae-2011-04i.fa",
>>>                "s_pombe-2011-04i.fa",
>>>                "y_lipolytica-2011-04i.fa");
>>>
>>> my $numberOfspecies = @species;
>>>
>>> # Run all n(n-1)/2 combinations without outgroup
>>> for (my $i = 0; $i < $numberOfspecies-1; $i++) {
>>>     for(my $j = $i+1; $j < $numberOfspecies; $j++) {
>>>     print "Staring inparanoid for: ".
>>> $species[$i]."\t".$species[$j]."\n";
>>>     system ("./inparanoid.pl ".$species[$i]."\t".$species[$j]."\n");
>>>     }
>>> }
>>>
>>> Regards,
>>> Mateusz
>>>
>>>
>>>
>>> On Tue, Oct 7, 2014 at 1:27 PM, Sammy Desilva <sammy.ich17 at gmail.com>
>>> wrote:
>>>
>>>> Dear Prof. Sonnhammer,
>>>>
>>>> I understand in case of 17 proteome I have to use multiparanoid for
>>>> clustering after computing 17*16/2 = 136 pairs with InParanoid. I wonder is
>>>> any script already available to automate the computations of multiple pairs
>>>> (here 136) with InParanoid for getting input for MultiParanoid?
>>>>
>>>> Regads
>>>> Sammy
>>>>
>>>>
>>>> On Mon, Sep 22, 2014 at 2:33 PM, Erik Sonnhammer <
>>>> erik.sonnhammer at scilifelab.se> wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> If you want ortholog groups that include all 17 species, InParanoid
>>>>> won't work. But if you only need pairwise relationships (which is usually
>>>>> the case) then it will.  Then you have to run InParanoid for all 17*16/2
>>>>> pairs.
>>>>>
>>>>> Erik Sonnhammer
>>>>>
>>>>> On 09/20/2014 11:32 AM, Sammy Desilva wrote:
>>>>>
>>>>> Hi, I want to assign orthology relationship among 17 proteomes. Could
>>>>> someone please suggest me how to do it offline in Inparanoid? The running
>>>>> command for such cases? I guess putting 3 organism it treats third as
>>>>> outgroup.
>>>>> Thanks
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> InParanoid mailing listInParanoid at lists.su.sehttps://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>>>
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> InParanoid mailing list
>>>> InParanoid at lists.su.se
>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>>
>>>>
>>>
>> _______________________________________________
>> InParanoid mailing list
>> InParanoid at lists.su.se
>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>
>
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From erik.sonnhammer at scilifelab.se  Sun Oct  4 15:18:42 2015
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Sun, 4 Oct 2015 15:18:42 +0200
Subject: [Inparanoid] low number of orthologs
In-Reply-To: <CA+LKX979YGAWZzVSdCc2JTt+MpNEwTjO=nvkYS_HHcCOy=VQiQ@mail.gmail.com>
References: <CA+LKX979YGAWZzVSdCc2JTt+MpNEwTjO=nvkYS_HHcCOy=VQiQ@mail.gmail.com>
Message-ID: <56112732.2000308@scilifelab.se>

Hi,

If you mean that you get 60 orthologs to S. cerevisiae then yes that is 
less than expected.  Are your 12000 protein sequences full-length?

You may have some technical problems with the sequence file that makes 
Blast choke, check for Blast errors.  How many homologs did you get (see 
inparanoid text output header)?

/Erik

On 09/29/2015 04:59 PM, Arjun Subedi wrote:
> Dear inparanoid developers,
>
> I am using inparanoid to derive orthologs for a newly sequenced 
> fungus. My organism consists 12000 protein sequence. When I run the 
> inparanoid with default settings against yeast (as protein B) it 
> yields only 60 orthologs, which I think is a very low number. Then I 
> splitted the sequence of both organism and took only half of the 
> sequences of each organism. Then I run a inparanoid, and it gives 
> higher no of othologs (214). Does it mean something wrong in my 
> sequence file or any other issues with bigger file?
>
> Thank you
>
> Arjun Subedi
>
>
> _______________________________________________
> InParanoid mailing list
> InParanoid at lists.su.se
> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se

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From erik.sonnhammer at scilifelab.se  Tue Oct  6 14:18:20 2015
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Tue, 6 Oct 2015 14:18:20 +0200
Subject: [Inparanoid] InParanoid of 1 protein
In-Reply-To: <CADDSWgKbpYMQrOJM-3Ea2zucOpe54A3YSE4q1ALivQUOBHzahw@mail.gmail.com>
References: <CADDSWg+Aj9CNcPUHRvpkOf2b2oPp7YHvW3oMh9y91ZRnJoG3ww@mail.gmail.com>
 <46722F38-02BA-4A24-BAAA-7AC2C76FC8DE@scilifelab.se>
 <CADDSWgKbpYMQrOJM-3Ea2zucOpe54A3YSE4q1ALivQUOBHzahw@mail.gmail.com>
Message-ID: <5613BC0C.1040708@scilifelab.se>

Dear Andrzej,

I'm afraid there is no facility in InParanoid to do that.

/Erik

On 10/02/2015 04:01 PM, Andrzej Zielezinski wrote:
> Dear Professor Sonnhammer,
>
> thank you for a quick reply. I'm aware that searching for orthologs 
> using the Reciprocal Best BLAST approach requires complete proteomes. 
> However, I don't have to BLAST all proteins in a proteome when I'm 
> interested only in one protein. I can BLAST a protein of interest 
> against a subject's complete proteome, then take a best hit and BLAST 
> it the other way against query's complete proteome. I was wondering 
> whether InParanoid can be used this way? For example, Reciprocal 
> Smallest Distance (RSD) approach lets users to find orthologs for 
> specific sequences in the query genome.
>
> Kindest regards,
> Andrzej ZIelezinski
>
>
> Andrzej Zielezinski, PhD
> Department of Computational Biology
> www: http://www.combio.pl
>
> On Fri, Oct 2, 2015 at 3:19 PM, Erik Sonnhammer 
> <erik.sonnhammer at scilifelab.se <mailto:erik.sonnhammer at scilifelab.se>> 
> wrote:
>
>     Hi, never use a subset - you need to use the complete proteomes
>     for the orthology assignments to be valid.
>
>     /Erik
>
>     On 02 Oct 2015, at 13:44, Andrzej Zielezinski <andrzejz at amu.edu.pl
>     <mailto:andrzejz at amu.edu.pl>> wrote:
>
>>     Dear Professor Sonnhammer,
>>
>>     thank you for sharing the standalone version of InParanoid.
>>
>>     I have a question regarding searching options in your software.
>>     Is it possible to search for orthologs/inparalogs only for
>>     specific sequences in the query genome. I would like to avoid a
>>     step where InParanoid calculates all-versus-all BLASTs of all
>>     proteins from query and subject genomes.
>>
>>     I would very much appreciate any guidance or advice you could
>>     provide on this matter.
>>
>>     Best regards,
>>     Andrzej ZIelezinski
>>
>>     ------------
>>     Andrzej Zielezinski, PhD
>>     Department of Computational Biology
>>     www: http://www.combio.pl
>>
>

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From megan.rees at mail.mcgill.ca  Tue Oct  6 16:12:16 2015
From: megan.rees at mail.mcgill.ca (Megan Rees)
Date: Tue, 6 Oct 2015 14:12:16 +0000
Subject: [Inparanoid] Adding a database to the Inparanoid web interface
Message-ID: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>

How can I request the addition of another organism to the Inparanoid web interface so that I can perform comparisons?


Thanks Megan
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From erik.sonnhammer at scilifelab.se  Tue Oct  6 16:16:38 2015
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Tue, 6 Oct 2015 16:16:38 +0200
Subject: [Inparanoid] Adding a database to the Inparanoid web interface
In-Reply-To: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
References: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
Message-ID: <5613D7C6.1030803@scilifelab.se>

Sure, but I can't estimate when it will appear.

Erik

On 10/06/2015 04:12 PM, Megan Rees wrote:
>
> How can I request the addition of another organism to the Inparanoid 
> web interface so that I can perform comparisons?
>
>
> Thanks Megan
>
>
>
> _______________________________________________
> InParanoid mailing list
> InParanoid at lists.su.se
> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se

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From megan.rees at mail.mcgill.ca  Tue Oct  6 16:25:55 2015
From: megan.rees at mail.mcgill.ca (Megan Rees)
Date: Tue, 6 Oct 2015 14:25:55 +0000
Subject: [Inparanoid] Adding a database to the Inparanoid web interface
In-Reply-To: <5613D7C6.1030803@scilifelab.se>
References: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>,
 <5613D7C6.1030803@scilifelab.se>
Message-ID: <CY1PR0301MB1610D0EA6E71DBA4DA15CD3FBE370@CY1PR0301MB1610.namprd03.prod.outlook.com>

Thank you Erik,


I would like to request the addition of

Mycobacterium kansasii ATCC 12478 including its plasmid. These have the Refseq identifiers of NC_022663.1<http://www.ncbi.nlm.nih.gov/nuccore/NC_022663.1> and NC_022654.1<http://www.ncbi.nlm.nih.gov/nuccore/NC_022654.1>. I can send you fasta files if that is helpful.

Can I assume that the Mycobacterium tuberculosis is the standard reference strain H37Rv?


Regards

Megan


________________________________
From: InParanoid <inparanoid-at-sbc.su.se-bounces at lists.su.se> on behalf of Erik Sonnhammer <erik.sonnhammer at scilifelab.se>
Sent: Tuesday, October 6, 2015 11:16 AM
To: inparanoid-at-sbc.su.se at lists.su.se
Subject: Re: [Inparanoid] Adding a database to the Inparanoid web interface

Sure, but I can't estimate when it will appear.

Erik

On 10/06/2015 04:12 PM, Megan Rees wrote:

How can I request the addition of another organism to the Inparanoid web interface so that I can perform comparisons?


Thanks Megan



_______________________________________________
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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From erik.sonnhammer at scilifelab.se  Tue Oct  6 16:50:08 2015
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Tue, 6 Oct 2015 16:50:08 +0200
Subject: [Inparanoid] Adding a database to the Inparanoid web interface
In-Reply-To: <CY1PR0301MB1610D0EA6E71DBA4DA15CD3FBE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
References: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
 <5613D7C6.1030803@scilifelab.se>
 <CY1PR0301MB1610D0EA6E71DBA4DA15CD3FBE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
Message-ID: <5613DFA0.3040709@scilifelab.se>

On 10/06/2015 04:25 PM, Megan Rees wrote:
>
> Thank you Erik,
>
>
> I would like to request the addition of
>
> Mycobacterium kansasii ATCC 12478 including its plasmid. These have 
> the Refseq identifiers of NC_022663.1 
> <http://www.ncbi.nlm.nih.gov/nuccore/NC_022663.1> and NC_022654.1 
> <http://www.ncbi.nlm.nih.gov/nuccore/NC_022654.1>. I can send you 
> fasta files if that is helpful.
>
> Can I assume that the Mycobacterium tuberculosis is the standard 
> reference strain H37Rv?
>
I guess not - clicking on the Uniprot link in the InParanoid Summary gives

Strains ^i <http://www.uniprot.org/help/taxonomy#strain> 	› 1254
› An03
› Canetti
› Isolate 50410, 50410
› Mt103


/Erik
>
>
> Regards
>
> Megan
>
>
>
> ------------------------------------------------------------------------
> *From:* InParanoid <inparanoid-at-sbc.su.se-bounces at lists.su.se> on 
> behalf of Erik Sonnhammer <erik.sonnhammer at scilifelab.se>
> *Sent:* Tuesday, October 6, 2015 11:16 AM
> *To:* inparanoid-at-sbc.su.se at lists.su.se
> *Subject:* Re: [Inparanoid] Adding a database to the Inparanoid web 
> interface
> Sure, but I can't estimate when it will appear.
>
> Erik
>
> On 10/06/2015 04:12 PM, Megan Rees wrote:
>>
>> How can I request the addition of another organism to the Inparanoid 
>> web interface so that I can perform comparisons?
>>
>>
>> Thanks Megan
>>
>>
>>
>> _______________________________________________
>> InParanoid mailing list
>> InParanoid at lists.su.se
>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>

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From megan.rees at mail.mcgill.ca  Tue Oct  6 17:46:54 2015
From: megan.rees at mail.mcgill.ca (Megan Rees)
Date: Tue, 6 Oct 2015 15:46:54 +0000
Subject: [Inparanoid] Adding a database to the Inparanoid web interface
In-Reply-To: <5613DFA0.3040709@scilifelab.se>
References: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
 <5613D7C6.1030803@scilifelab.se>
 <CY1PR0301MB1610D0EA6E71DBA4DA15CD3FBE370@CY1PR0301MB1610.namprd03.prod.outlook.com>,
 <5613DFA0.3040709@scilifelab.se>
Message-ID: <CY1PR0301MB1610A29A95B6372E0E387CB2BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>

Yes - I was a bit puzzled by that as the database list doesn't indicate that it is the reference strain but I tried a practice search against another species and when clicking on the Mtb proteins identified the Uniprot link takes me to the protein for M.tb H37Rv.


So could I also then request Mycobacterium tuberculosis h37Rv to also be added the RefSeq identifier is  NC_000962.3<http://www.ncbi.nlm.nih.gov/nuccore/NC_000962.3> ?


Thanks Megan


________________________________
From: InParanoid <inparanoid-at-sbc.su.se-bounces at lists.su.se> on behalf of Erik Sonnhammer <erik.sonnhammer at scilifelab.se>
Sent: Tuesday, October 6, 2015 11:50 AM
To: inparanoid-at-sbc.su.se at lists.su.se
Subject: Re: [Inparanoid] Adding a database to the Inparanoid web interface

On 10/06/2015 04:25 PM, Megan Rees wrote:

Thank you Erik,


I would like to request the addition of

Mycobacterium kansasii ATCC 12478 including its plasmid. These have the Refseq identifiers of NC_022663.1<http://www.ncbi.nlm.nih.gov/nuccore/NC_022663.1> and NC_022654.1<http://www.ncbi.nlm.nih.gov/nuccore/NC_022654.1>. I can send you fasta files if that is helpful.

Can I assume that the Mycobacterium tuberculosis is the standard reference strain H37Rv?

I guess not - clicking on the Uniprot link in the InParanoid Summary gives

Strains i<http://www.uniprot.org/help/taxonomy#strain>  > 1254
> An03
> Canetti
> Isolate 50410, 50410
> Mt103

/Erik


Regards

Megan


________________________________
From: InParanoid <inparanoid-at-sbc.su.se-bounces at lists.su.se><mailto:inparanoid-at-sbc.su.se-bounces at lists.su.se> on behalf of Erik Sonnhammer <erik.sonnhammer at scilifelab.se><mailto:erik.sonnhammer at scilifelab.se>
Sent: Tuesday, October 6, 2015 11:16 AM
To: inparanoid-at-sbc.su.se at lists.su.se<mailto:inparanoid-at-sbc.su.se at lists.su.se>
Subject: Re: [Inparanoid] Adding a database to the Inparanoid web interface

Sure, but I can't estimate when it will appear.

Erik

On 10/06/2015 04:12 PM, Megan Rees wrote:

How can I request the addition of another organism to the Inparanoid web interface so that I can perform comparisons?


Thanks Megan



_______________________________________________
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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From erik.sonnhammer at scilifelab.se  Wed Oct  7 20:59:34 2015
From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer)
Date: Wed, 7 Oct 2015 20:59:34 +0200
Subject: [Inparanoid] Adding a database to the Inparanoid web interface
In-Reply-To: <CY1PR0301MB1610A29A95B6372E0E387CB2BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
References: <CY1PR0301MB16100199652E259E1BAEE318BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
 <5613D7C6.1030803@scilifelab.se>
 <CY1PR0301MB1610D0EA6E71DBA4DA15CD3FBE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
 <5613DFA0.3040709@scilifelab.se>
 <CY1PR0301MB1610A29A95B6372E0E387CB2BE370@CY1PR0301MB1610.namprd03.prod.outlook.com>
Message-ID: <56156B96.5090805@scilifelab.se>

Yes, but bear in mind that InParanoid is oriented towards eukaryotes.  
The only prokaryotes that are included right now are there because they 
are part of the Quest for Orthologs Consortium's reference proteomes.  
In other words, it is unlikely that we will included two M. tuberculosis.

Bests
Erik

On 2015-10-06 17:46, Megan Rees wrote:
>
> Yes - I was a bit puzzled by that as the database list doesn't 
> indicate that it is the reference strain but I tried a practice search 
> against another species and when clicking on the Mtb proteins 
> identified the Uniprot link takes me to the protein for M.tb H37Rv.
>
>
> So could I also then request Mycobacterium tuberculosis h37Rv to also 
> be added the RefSeq identifier is NC_000962.3 
> <http://www.ncbi.nlm.nih.gov/nuccore/NC_000962.3> ?
>
>
> Thanks Megan
>
>
>
> ------------------------------------------------------------------------
> *From:* InParanoid <inparanoid-at-sbc.su.se-bounces at lists.su.se> on 
> behalf of Erik Sonnhammer <erik.sonnhammer at scilifelab.se>
> *Sent:* Tuesday, October 6, 2015 11:50 AM
> *To:* inparanoid-at-sbc.su.se at lists.su.se
> *Subject:* Re: [Inparanoid] Adding a database to the Inparanoid web 
> interface
> On 10/06/2015 04:25 PM, Megan Rees wrote:
>>
>> Thank you Erik,
>>
>>
>> I would like to request the addition of
>>
>> Mycobacterium kansasii ATCC 12478 including its plasmid. These have 
>> the Refseq identifiers of NC_022663.1 
>> <http://www.ncbi.nlm.nih.gov/nuccore/NC_022663.1> and NC_022654.1 
>> <http://www.ncbi.nlm.nih.gov/nuccore/NC_022654.1>. I can send you 
>> fasta files if that is helpful.
>>
>> Can I assume that the Mycobacterium tuberculosis is the standard 
>> reference strain H37Rv?
>>
> I guess not - clicking on the Uniprot link in the InParanoid Summary gives
>
> Strains ^i <http://www.uniprot.org/help/taxonomy#strain> 	› 1254
> › An03
> › Canetti
> › Isolate 50410, 50410
> › Mt103
>
>
> /Erik
>>
>>
>> Regards
>>
>> Megan
>>
>>
>>
>> ------------------------------------------------------------------------
>> *From:* InParanoid <inparanoid-at-sbc.su.se-bounces at lists.su.se> on 
>> behalf of Erik Sonnhammer <erik.sonnhammer at scilifelab.se>
>> *Sent:* Tuesday, October 6, 2015 11:16 AM
>> *To:* inparanoid-at-sbc.su.se at lists.su.se
>> *Subject:* Re: [Inparanoid] Adding a database to the Inparanoid web 
>> interface
>> Sure, but I can't estimate when it will appear.
>>
>> Erik
>>
>> On 10/06/2015 04:12 PM, Megan Rees wrote:
>>>
>>> How can I request the addition of another organism to the Inparanoid 
>>> web interface so that I can perform comparisons?
>>>
>>>
>>> Thanks Megan
>>>
>>>
>>>
>>> _______________________________________________
>>> InParanoid mailing list
>>> InParanoid at lists.su.se
>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>
>

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From sammy.ich17 at gmail.com  Thu Oct  8 16:56:48 2015
From: sammy.ich17 at gmail.com (Sammy Desilva)
Date: Thu, 8 Oct 2015 16:56:48 +0200
Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid
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 <CAPf=4Rf4vWPWiHAA9Pz=Np2i0d3bUspdtd1rX-AZMTsc8NJx_Q@mail.gmail.com>
 <CAJXH_1MWGaETkJBCtD+6_Sx5dwjQKx_1GBPZVw5ZkvbpAETHHg@mail.gmail.com>
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Message-ID: <CAJXH_1NSpi_NAGwbqtuhLt15fRLkaOa0qnm8z0_2GP5x=u_i-g@mail.gmail.com>

Could someone face this same "SeqPortNew blast error" before which is
affecting my computations? How can I solve this?

On 10/1/15, Sammy Desilva <sammy.ich17 at gmail.com> wrote:
> Dear all,
>
> So finally I canceled the computations. Can you please check the error log
> file (attached) and let me know
> what exactly is the problem?
>
>
> *Thanks*
> *Sammy*
>
> On Tue, Sep 29, 2015 at 4:53 PM, Verena Haunschmid <veroamilbe at gmail.com>
> wrote:
>
>> Dear Sammy,
>>
>> I once did comparisons of several organisms and had the same problem as
>>  you. To speed it up a little bit I precomputed the blast files since
>> that
>> is the most time consuming step as far as I remember.
>>
>> And if you do comparisons A-B, A-C, B-C, ... you would need to compute
>> the
>> blast output for A-A, B-B, C-C several times and that's half of the
>> computation time for each pairwise comparison. Just compute all blast
>> files
>> for each organism with itself and uncomment those lines in the perl
>> script.
>> (might be that I still have these script, I will check later...)
>>
>> Best regards,
>> Verena
>>
>>
>>
>> On Tue, Sep 29, 2015 at 4:46 PM Sammy Desilva <sammy.ich17 at gmail.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> I am again starting this thread here again. At that time I finally
>>> shifted to normal PC instead of cluster. Now, I am analyzing 29 proteome
>>> for orthology with multiparanoid. I used  the above script with sbatch
>>> seq
>>> array in slurm but it  is still not finished in 15 days. Is there any
>>> alternative way exist for doing this computations/
>>>
>>> Thnaks
>>>
>>> On Tue, Oct 7, 2014 at 1:39 PM, mateusz.kaduk at gmail.com <
>>> mateusz.kaduk at gmail.com> wrote:
>>>
>>>> Dear Sammy,
>>>>
>>>> There is no script with inparanoid to automate pairwise runs, but I am
>>>> using the following code to run all n(n-1)/2 pairwise comparisons
>>>> without
>>>> outgroup, it's just few lines of code, but maybe you will find it
>>>> useful.
>>>>
>>>> #!/usr/bin/perl
>>>> use strict;
>>>> use warnings;
>>>>
>>>> # Here is the list of fasta files in the same directory as
>>>> inparanoid.pl
>>>> my @species = ("c_albicans-2011-04i.fa",
>>>>                "c_neoformans-2011-04i.fa",
>>>>                "s_cerevisiae-2011-04i.fa",
>>>>                "s_pombe-2011-04i.fa",
>>>>                "y_lipolytica-2011-04i.fa");
>>>>
>>>> my $numberOfspecies = @species;
>>>>
>>>> # Run all n(n-1)/2 combinations without outgroup
>>>> for (my $i = 0; $i < $numberOfspecies-1; $i++) {
>>>>     for(my $j = $i+1; $j < $numberOfspecies; $j++) {
>>>>     print "Staring inparanoid for: ".
>>>> $species[$i]."\t".$species[$j]."\n";
>>>>     system ("./inparanoid.pl ".$species[$i]."\t".$species[$j]."\n");
>>>>     }
>>>> }
>>>>
>>>> Regards,
>>>> Mateusz
>>>>
>>>>
>>>>
>>>> On Tue, Oct 7, 2014 at 1:27 PM, Sammy Desilva <sammy.ich17 at gmail.com>
>>>> wrote:
>>>>
>>>>> Dear Prof. Sonnhammer,
>>>>>
>>>>> I understand in case of 17 proteome I have to use multiparanoid for
>>>>> clustering after computing 17*16/2 = 136 pairs with InParanoid. I
>>>>> wonder is
>>>>> any script already available to automate the computations of multiple
>>>>> pairs
>>>>> (here 136) with InParanoid for getting input for MultiParanoid?
>>>>>
>>>>> Regads
>>>>> Sammy
>>>>>
>>>>>
>>>>> On Mon, Sep 22, 2014 at 2:33 PM, Erik Sonnhammer <
>>>>> erik.sonnhammer at scilifelab.se> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> If you want ortholog groups that include all 17 species, InParanoid
>>>>>> won't work. But if you only need pairwise relationships (which is
>>>>>> usually
>>>>>> the case) then it will.  Then you have to run InParanoid for all
>>>>>> 17*16/2
>>>>>> pairs.
>>>>>>
>>>>>> Erik Sonnhammer
>>>>>>
>>>>>> On 09/20/2014 11:32 AM, Sammy Desilva wrote:
>>>>>>
>>>>>> Hi, I want to assign orthology relationship among 17 proteomes. Could
>>>>>> someone please suggest me how to do it offline in Inparanoid? The
>>>>>> running
>>>>>> command for such cases? I guess putting 3 organism it treats third as
>>>>>> outgroup.
>>>>>> Thanks
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> InParanoid mailing
>>>>>> listInParanoid at lists.su.sehttps://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> InParanoid mailing list
>>>>> InParanoid at lists.su.se
>>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>>>
>>>>>
>>>>
>>> _______________________________________________
>>> InParanoid mailing list
>>> InParanoid at lists.su.se
>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se
>>>
>>
>

From alyamahmoud at gmail.com  Wed Oct 21 11:19:21 2015
From: alyamahmoud at gmail.com (Alyaa Mahmoud)
Date: Wed, 21 Oct 2015 12:19:21 +0300
Subject: [Inparanoid] Non orthologous groups
Message-ID: <BFFA2C42-B408-4B0D-B349-FB792E5DB5A8@gmail.com>

Dear inparanoid team 

I would like to ask if its possible to extract non-orthologous groups from inparanoid output. Is this possible ?

Thanks a lot
Alyaa