From sammy.ich17 at gmail.com Tue Oct 7 13:27:56 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Tue, 7 Oct 2014 13:27:56 +0200 Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid In-Reply-To: <54201701.2050607@scilifelab.se> References: <54201701.2050607@scilifelab.se> Message-ID: 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 > > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From mateusz.kaduk at gmail.com Tue Oct 7 13:39:52 2014 From: mateusz.kaduk at gmail.com (mateusz.kaduk at gmail.com) Date: Tue, 7 Oct 2014 13:39:52 +0200 Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid In-Reply-To: References: <54201701.2050607@scilifelab.se> Message-ID: 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 elserj at science.oregonstate.edu Tue Oct 14 23:57:15 2014 From: elserj at science.oregonstate.edu (Justin Elser) Date: Tue, 14 Oct 2014 14:57:15 -0700 Subject: [Inparanoid] Missing specific genes from InParanoid results Message-ID: <543D9C3B.4070907@science.oregonstate.edu> I am running InParanoid 3.0 (although I also tested under 4.1 to see if it fixed my problem) and have the following issue. I am running Arabidopsis thaliana vs Oryza sativa sp. japonica and mostly getting results as I would expect. However, a few genes end up not getting placed in a cluster at all, even though it looks like the blast results show pretty good matches. I have placed grepped blast results for AT5G49190 at the end of this message. If I am understanding the scoring correctly, this gene shows a high similarity score with AT4G02280 and OS03T0340500-01, which is what I expect from an independent analysis using Compara (74% match). However, when the script to place the genes in clusters is ran, AT5G49190 does not show up in any cluster at all. There is a cluster that does contain AT4G02280 and OS03T0340500-01. I'm hoping you guys can help me figure out what is causing this. Also, I thought I tried to subscribe to the mailing list last week, but haven't seen anything back yet. If someone could check on this and let me know if I missed something in my attempt, that would be great. Let me know if you need any more information or things I can do to diagnose this. Thanks in advance, justin [elserj at waterman ]$ cat Arabidopsis_thaliana_phytozome_mart_9_9_13.fa-Arabidopsis_thaliana_phytozome_mart_9_9_13.fa | grep AT5G49190 AT5G37180.1 AT5G49190.1 894.0 836 807 788 791 788 791 q:14-801 h:15-805 AT4G10120.2 AT5G49190.1 166.4 1050 807 494 485 494 485 q:197-690 h:278-762 AT1G78800.1 AT5G49190.1 60.8 403 807 177 188 177 188 q:213-389 h:573-760 AT4G10120.1 AT5G49190.1 166.4 1050 807 494 485 494 485 q:197-690 h:278-762 AT4G02280.1 AT5G49190.1 1293.5 809 807 802 802 802 802 q:8-809 h:5-806 AT5G20830.2 AT5G49190.1 1139.8 808 807 799 802 799 802 q:10-808 h:5-806 AT1G73370.1 AT5G49190.1 932.2 942 807 803 802 803 802 q:11-813 h:5-806 AT5G49190.1 AT5G49190.1 1676.8 807 807 807 807 807 807 q:1-807 h:1-807 AT5G49190.1 AT4G02280.1 1293.5 807 809 802 802 802 802 q:5-806 h:8-809 AT5G49190.1 AT3G43190.1 1152.1 807 808 802 799 802 799 q:5-806 h:10-808 AT5G49190.1 AT5G20830.1 1124.4 807 808 802 799 802 799 q:5-806 h:10-808 AT5G49190.1 AT5G20830.2 1124.4 807 808 802 799 802 799 q:5-806 h:10-808 AT5G49190.1 AT1G73370.1 932.2 807 942 802 803 802 803 q:5-806 h:11-813 AT5G49190.1 AT1G73370.2 917.5 807 898 768 769 768 769 q:39-806 h:1-769 AT5G49190.1 AT5G37180.1 895.2 807 836 791 788 791 788 q:15-805 h:14-801 AT5G49190.1 AT4G10120.1 164.1 807 1050 485 494 485 494 q:278-762 h:197-690 AT5G49190.1 AT4G10120.2 164.1 807 1050 485 494 485 494 q:278-762 h:197-690 AT5G49190.1 AT5G11110.1 159.1 807 1047 496 504 496 504 q:278-773 h:177-680 AT5G49190.1 AT1G04920.1 151.8 807 1062 485 500 485 500 q:278-762 h:172-671 AT5G49190.1 AT5G20280.1 145.6 807 1043 494 507 494 507 q:278-771 h:170-676 AT5G49190.1 AT1G78800.1 60.8 807 403 188 177 188 177 q:573-760 h:213-389 AT1G04920.1 AT5G49190.1 151.8 1062 807 500 485 500 485 q:172-671 h:278-762 AT1G73370.2 AT5G49190.1 917.5 898 807 769 768 769 768 q:1-769 h:39-806 AT5G11110.1 AT5G49190.1 159.1 1047 807 504 496 504 496 q:177-680 h:278-773 AT5G20280.1 AT5G49190.1 149.4 1043 807 507 494 507 494 q:170-676 h:278-771 AT5G20830.1 AT5G49190.1 1139.8 808 807 799 802 799 802 q:10-808 h:5-806 AT3G43190.1 AT5G49190.1 1152.1 808 807 799 802 799 802 q:10-808 h:5-806 [elserj at waterman ]$ cat Arabidopsis_thaliana_phytozome_mart_9_9_13.fa-Oryza_sativa.japonica.IRGSP_gramene_ftp_1_17_14.fa | grep AT5G49190 AT5G49190.1 OS03T0340500-01 1285.0 807 809 802 800 802 800 q:5-806 h:8-807 AT5G49190.1 OS06T0194900-03 1183.7 807 808 802 797 802 797 q:4-805 h:6-802 AT5G49190.1 OS06T0194900-02 1183.7 807 808 802 797 802 797 q:4-805 h:6-802 AT5G49190.1 OS06T0194900-01 1183.7 807 808 802 797 802 797 q:4-805 h:6-802 AT5G49190.1 OS03T0401300-01 1170.6 807 816 801 799 801 799 q:5-805 h:12-810 AT5G49190.1 OS07T0616800-01 1162.9 807 816 801 799 801 799 q:5-805 h:12-810 AT5G49190.1 OS06T0194900-04 992.6 807 649 644 643 644 643 q:162-805 h:1-643 AT5G49190.1 OS04T0309600-01 921.0 807 844 803 794 803 794 q:5-807 h:9-802 AT5G49190.1 OS04T0249500-00 920.2 807 844 802 793 802 793 q:5-806 h:9-801 AT5G49190.1 OS02T0831500-01 913.7 807 846 797 798 797 798 q:5-801 h:7-804 AT5G49190.1 OS03T0401300-02 481.5 807 315 310 309 310 309 q:496-805 h:1-309 AT5G49190.1 OS03T0340500-03 449.9 807 278 276 276 276 276 q:531-806 h:1-276 AT5G49190.1 OS03T0401300-03 203.8 807 132 126 126 126 126 q:680-805 h:1-126 AT5G49190.1 OS08T0301500-01 162.9 807 1066 494 507 494 507 q:278-771 h:188-694 AT5G49190.1 OS02T0184400-03 150.2 807 963 506 524 506 524 q:259-764 h:133-656 AT5G49190.1 OS02T0184400-02 150.2 807 963 506 524 506 524 q:259-764 h:133-656 AT5G49190.1 OS02T0184400-01 150.2 807 1011 506 524 506 524 q:259-764 h:181-704 AT5G49190.1 OS02T0184400-04 111.7 807 595 293 288 293 288 q:472-764 h:1-288 AT5G49190.1 OS11T0236100-01 84.0 807 509 143 135 143 135 q:630-772 h:4-138 [elserj at waterman ]$ cat Oryza_sativa.japonica.IRGSP_gramene_ftp_1_17_14.fa-Arabidopsis_thaliana_phytozome_mart_9_9_13.fa | grep AT5G49190 OS02T0184400-01 AT5G49190.1 150.2 1011 807 524 506 524 506 q:181-704 h:259-764 OS02T0184400-02 AT5G49190.1 150.2 963 807 524 506 524 506 q:133-656 h:259-764 OS02T0184400-03 AT5G49190.1 150.2 963 807 524 506 524 506 q:133-656 h:259-764 OS02T0184400-04 AT5G49190.1 111.7 595 807 288 293 288 293 q:1-288 h:472-764 OS02T0831500-01 AT5G49190.1 913.7 846 807 798 797 798 797 q:7-804 h:5-801 OS03T0340500-01 AT5G49190.1 1285.0 809 807 800 802 800 802 q:8-807 h:5-806 OS03T0340500-03 AT5G49190.1 449.9 278 807 276 276 276 276 q:1-276 h:531-806 OS03T0401300-01 AT5G49190.1 1170.6 816 807 799 801 799 801 q:12-810 h:5-805 OS03T0401300-02 AT5G49190.1 481.5 315 807 309 310 309 310 q:1-309 h:496-805 OS03T0401300-03 AT5G49190.1 203.8 132 807 126 126 126 126 q:1-126 h:680-805 OS04T0249500-00 AT5G49190.1 920.2 844 807 793 802 793 802 q:9-801 h:5-806 OS04T0309600-01 AT5G49190.1 921.0 844 807 794 803 794 803 q:9-802 h:5-807 OS06T0194900-01 AT5G49190.1 1183.7 808 807 797 802 797 802 q:6-802 h:4-805 OS06T0194900-02 AT5G49190.1 1183.7 808 807 797 802 797 802 q:6-802 h:4-805 OS06T0194900-03 AT5G49190.1 1183.7 808 807 797 802 797 802 q:6-802 h:4-805 OS06T0194900-04 AT5G49190.1 992.6 649 807 643 644 643 644 q:1-643 h:162-805 OS07T0616800-01 AT5G49190.1 1162.9 816 807 799 801 799 801 q:12-810 h:5-805 OS08T0301500-01 AT5G49190.1 162.2 1066 807 507 494 507 494 q:188-694 h:278-771 OS11T0236100-01 AT5G49190.1 83.2 509 807 135 143 135 143 q:4-138 h:630-772 -- ********************************************************** * * * Justin Elser * * Computational Biology Post Doc * * Dept. of Botany and Plant Pathology * * Oregon State University * * * * email: elserj at science.oregonstate.edu * * internet: www.science.oregonstate.edu/~elserj * * * **********************************************************