From pengchy at gmail.com Mon Sep 28 16:42:53 2015 From: pengchy at gmail.com (Pengcheng Yang) Date: Mon, 28 Sep 2015 22:42:53 +0800 Subject: [Inparanoid] confidence value cutoff Message-ID: <560951ED.9090802@gmail.com> Hi Inparanoid developers, I am using Inparanoid to cluster proteins into groups to identify ortholog genes. However, I have a questions about the confidence value cutoff. Is it too low, default 0.05 to increase the false positive? What is the optimized value you recommend? Thank you and best wishes, -- Pengcheng Yang (杨鹏程) Research Associate Beijing Institute of Life Science, Chinese Academy of Sciences Beijing, People's Republic of China Email: yangpc at biols.ac.cn From erik.sonnhammer at scilifelab.se Mon Sep 28 18:46:12 2015 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 28 Sep 2015 18:46:12 +0200 Subject: [Inparanoid] confidence value cutoff In-Reply-To: <560951ED.9090802@gmail.com> References: <560951ED.9090802@gmail.com> Message-ID: <56096ED4.8030808@scilifelab.se> Hi, 0.05 is "optimised for coverage". We have not actually done any proper optimisation of it, but we know that the false positive rate is low at this value, so one could even try to lower it. But if you only want the very strongest orthologs then you can increase it. On http://orthology.benchmarkservice.org we use default cutoff and 1.0. The main effect is that 1.0 gives much lower coverage. Sometimes 1.0 has better accuracy but sometimes not. So unless you are particularly interested in 1-1 orthologs I recommend leaving it at 0.05. Erik Sonnhammer On 2015-09-28 16:42, Pengcheng Yang wrote: > Hi Inparanoid developers, > > I am using Inparanoid to cluster proteins into groups to identify > ortholog genes. However, I have a questions about the confidence value > cutoff. Is it too low, default 0.05 to increase the false positive? > What is the optimized value you recommend? > > Thank you and best wishes, > From yangpc at biols.ac.cn Tue Sep 29 01:51:19 2015 From: yangpc at biols.ac.cn (Pengcheng Yang) Date: Tue, 29 Sep 2015 07:51:19 +0800 Subject: [Inparanoid] confidence value cutoff In-Reply-To: <56096ED4.8030808@scilifelab.se> References: <560951ED.9090802@gmail.com> <56096ED4.8030808@scilifelab.se> Message-ID: <5609D277.9010505@biols.ac.cn> Hi Erik Sonnhammer, Thank you for your reply. One phenomenon is found that for the two organisms A and B with A-1 and B-1, B-2 proteins, respectively. These three proteins clustered into one ortholog group. I found that the parsed blast results contain the hit records between A-1 and B-1, B-1 and B-2, but not A-1 and B-2. However, this is possible because blast_parser.pl set several criteria to filtering the alignment. Ok, I will leave it at 0.05. Thank you. Pengcheng On 2015/9/29 0:46, Erik Sonnhammer wrote: > Hi, > > 0.05 is "optimised for coverage". We have not actually done any proper > optimisation of it, but we know that the false positive rate is low at > this value, so one could even try to lower it. But if you only want > the very strongest orthologs then you can increase it. On > http://orthology.benchmarkservice.org we use default cutoff and 1.0. > The main effect is that 1.0 gives much lower coverage. Sometimes 1.0 > has better accuracy but sometimes not. So unless you are particularly > interested in 1-1 orthologs I recommend leaving it at 0.05. > > Erik Sonnhammer > > On 2015-09-28 16:42, Pengcheng Yang wrote: >> Hi Inparanoid developers, >> >> I am using Inparanoid to cluster proteins into groups to identify >> ortholog genes. However, I have a questions about the confidence >> value cutoff. Is it too low, default 0.05 to increase the false >> positive? What is the optimized value you recommend? >> >> Thank you and best wishes, >> > > _______________________________________________ > InParanoid mailing list > InParanoid at lists.su.se > https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se From sammy.ich17 at gmail.com Tue Sep 29 16:45:16 2015 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Tue, 29 Sep 2015 16:45:16 +0200 Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid In-Reply-To: References: <54201701.2050607@scilifelab.se> Message-ID: 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 > 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 >> >> > -------------- next part -------------- An HTML attachment was scrubbed... URL: From subediarju at gmail.com Tue Sep 29 16:59:16 2015 From: subediarju at gmail.com (Arjun Subedi) Date: Tue, 29 Sep 2015 09:59:16 -0500 Subject: [Inparanoid] low number of orthologs Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: