[Inparanoid] Analyzing 17 proteome orthology with Inparanoid

[Sammy Desilva]

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
>>>
>>>
>>>
>>
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>>
>
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