From bbely at ebi.ac.uk Tue Sep 16 16:17:55 2014 From: bbely at ebi.ac.uk (Benoit BELY) Date: Tue, 16 Sep 2014 15:17:55 +0100 Subject: [Inparanoid] Massive increase of InParanoid mapping to UniProtKB Message-ID: <54184693.1080605@ebi.ac.uk> Hi there, I tried to contact Thomas Schmitt be my email returned with failed to deliver error. Can someone else have a look at it for me please ? I noticed that now the mapping file you provide to us is gziped now. http://inparanoid.sbc.su.se/download/current/InParanoidUniProtXref.txt.gz, so I changed our procedure to use this new file. I also noticed that your number of link to UniProtKB has jump a lot : UPDATED: 2916242 DRs (1047.32% added, 27.05% removed) I went to your website expecting a new release, but it says there December 2013. Can you confirm you expected this to happen before we commit the changes to our database please ? Thanks Ben -- Benoit BELY ---------------------------------------- Software Engineer - UniProt release production team European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom PHONE:+ (0) 1223 49 2648 FAX:+ (0) 1223 494 468 URL:http://www.ebi.ac.uk/ ---------------------------------------- The urgent is done, the impossible is underway, miracles allow time From sammy.ich17 at gmail.com Thu Sep 18 03:19:56 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Thu, 18 Sep 2014 03:19:56 +0200 Subject: [Inparanoid] Problem with Inparanoid groups Message-ID: Hello, I downloaded the latest version of Inparanoid8 on my Ubuntu 12.1 and ran Inparanoid on 2 big proteome. On the default paramete the algorithm resulted only 70 groups while when I used orthomcl on same dataset it resulted around 3000 groups. Please let me know what i am doing wrong? Thanks Sam -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Thu Sep 18 10:24:49 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Thu, 18 Sep 2014 10:24:49 +0200 Subject: [Inparanoid] Problem with Inparanoid groups In-Reply-To: References: Message-ID: <541A96D1.4010505@scilifelab.se> Hi, probably something went wrong with Blast. In the beginning of the output file Output.xxx you can see how many homologs were detected by Blast, that will probably tell you what went wrong. Erik Sonnhammer On 09/18/2014 03:19 AM, Sammy Desilva wrote: > Hello, > > I downloaded the latest version of Inparanoid8 on my Ubuntu 12.1 > and ran Inparanoid on 2 big proteome. On the default paramete the > algorithm resulted only 70 groups while when I used orthomcl on same > dataset it resulted around 3000 groups. > Please let me know what i am doing wrong? > > Thanks > Sam > > > _______________________________________________ > 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 erik.sonnhammer at scilifelab.se Thu Sep 18 11:12:28 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Thu, 18 Sep 2014 11:12:28 +0200 Subject: [Inparanoid] Problem with Inparanoid groups In-Reply-To: References: <541A96D1.4010505@scilifelab.se> Message-ID: <541AA1FC.4040908@scilifelab.se> Well clearly you can't expect more than 71 orthologs if that's how many homologs Blast finds. My guess is that your sequences are not read properly by Blast. Erik On 09/18/2014 10:45 AM, Sammy Desilva wrote: > This is my truncated output: > > 18651 sequences in file int1.fasta > 9630 sequences in file afum.fasta > 143 sequences int1.fasta have homologs in dataset afum.fasta > 71 sequences afum.fasta have homologs in dataset int1.fasta > 184 int1.fasta-int1.fasta matches > 101 afum.fasta-afum.fasta matches > ################################### > 66 groups of orthologs > 87 in-paralogs from int1.fasta > 77 in-paralogs from afum.fasta > Grey zone 0 bits > Score cutoff 40 bits > In-paralogs with confidence less than 0.05 not shown > Sequence overlap cutoff 0.5 > Group merging cutoff 0.5 > Scoring matrix BLOSUM62 > ################################### > ___________________________________________________________________________________ > Group of orthologs #1. Best score 122 bits > Score difference with first non-orthologous sequence - int1.fasta:3 > afum.fasta:122 > int1|P04914 100.00% afum|XP_752748.1 100.00% > afum|XP_755719.2 85.71% > Bootstrap support for int1|P04914 as seed ortholog is 100%. > Bootstrap support for afum|XP_752748.1 as seed ortholog is 100%. > .. > Score difference with first non-orthologous sequence - int1.fasta:41 > afum.fasta:41 > int1|Q9VTE5 100.00% afum|XP_750133.1 100.00% > Bootstrap support for int1|Q9VTE5 as seed ortholog is 100%. > Bootstrap support for afum|XP_750133.1 as seed ortholog is 100%. > > This is the Screen LOG for other analysis with similar problem: > > sam28 at wbbi180:~/opt/inparanoid/int2_afum$ perl inparanoid.pl > int2.fasta afum.fasta > 18486 sequences in file int2.fasta > 9096 sequences in file afum.fasta > Trying to run BLAST now - this may take several hours ... or days in > worst case! > Formatting BLAST databases > Done formatting > Starting BLAST searches... > > Starting first BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 > 18:12:38 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > > > Starting second BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 > 20:05:44 CEST 2014 > do_ypcall: clnt_call: RPC: Timed out > > Starting first BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 > 20:22:59 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > > Starting second BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 > 21:03:38 CEST 2014 > > Starting first BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 > 21:11:10 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > > Starting second BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 > 21:52:14 CEST 2014 > > Starting first BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 > 21:56:03 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > > Starting second BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 > 22:18:41 CEST 2014 > do_ypcall: clnt_call: RPC: Timed out > Done BLAST searches. Starting ortholog detection... > Output saved to file Output.int2.fasta-afum.fasta > HTML output saved to orthologs.int2.fasta-afum.fasta.html > Table output saved to table.int2.fasta-afum.fasta > mysql output saved to sqltable.int2.fasta-afum.fasta > sam28 at wbbi180:~/opt/inparanoid/int2_afum$ > > > 2014-09-18 10:24 GMT+02:00 Erik Sonnhammer > >: > > Hi, probably something went wrong with Blast. > > In the beginning of the output file Output.xxx you can see how > many homologs were detected by Blast, that will probably tell you > what went wrong. > > Erik Sonnhammer > > > On 09/18/2014 03:19 AM, Sammy Desilva wrote: >> Hello, >> >> I downloaded the latest version of Inparanoid8 on my Ubuntu 12.1 >> and ran Inparanoid on 2 big proteome. On the default paramete the >> algorithm resulted only 70 groups while when I used orthomcl on >> same dataset it resulted around 3000 groups. >> Please let me know what i am doing wrong? >> >> Thanks >> Sam >> >> >> _______________________________________________ >> 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 sammy.ich17 at gmail.com Thu Sep 18 10:45:02 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Thu, 18 Sep 2014 10:45:02 +0200 Subject: [Inparanoid] Problem with Inparanoid groups In-Reply-To: <541A96D1.4010505@scilifelab.se> References: <541A96D1.4010505@scilifelab.se> Message-ID: This is my truncated output: 18651 sequences in file int1.fasta 9630 sequences in file afum.fasta 143 sequences int1.fasta have homologs in dataset afum.fasta 71 sequences afum.fasta have homologs in dataset int1.fasta 184 int1.fasta-int1.fasta matches 101 afum.fasta-afum.fasta matches ################################### 66 groups of orthologs 87 in-paralogs from int1.fasta 77 in-paralogs from afum.fasta Grey zone 0 bits Score cutoff 40 bits In-paralogs with confidence less than 0.05 not shown Sequence overlap cutoff 0.5 Group merging cutoff 0.5 Scoring matrix BLOSUM62 ################################### ___________________________________________________________________________________ Group of orthologs #1. Best score 122 bits Score difference with first non-orthologous sequence - int1.fasta:3 afum.fasta:122 int1|P04914 100.00% afum|XP_752748.1 100.00% afum|XP_755719.2 85.71% Bootstrap support for int1|P04914 as seed ortholog is 100%. Bootstrap support for afum|XP_752748.1 as seed ortholog is 100%. .. Score difference with first non-orthologous sequence - int1.fasta:41 afum.fasta:41 int1|Q9VTE5 100.00% afum|XP_750133.1 100.00% Bootstrap support for int1|Q9VTE5 as seed ortholog is 100%. Bootstrap support for afum|XP_750133.1 as seed ortholog is 100%. This is the Screen LOG for other analysis with similar problem: sam28 at wbbi180:~/opt/inparanoid/int2_afum$ perl inparanoid.pl int2.fasta afum.fasta 18486 sequences in file int2.fasta 9096 sequences in file afum.fasta Trying to run BLAST now - this may take several hours ... or days in worst case! Formatting BLAST databases Done formatting Starting BLAST searches... Starting first BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 18:12:38 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Starting second BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 20:05:44 CEST 2014 do_ypcall: clnt_call: RPC: Timed out Starting first BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 20:22:59 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Starting second BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 21:03:38 CEST 2014 Starting first BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 21:11:10 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Selenocysteine (U) at position 37 replaced by X Starting second BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 21:52:14 CEST 2014 Starting first BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 21:56:03 CEST 2014 [blastall] WARNING: the -C 3 argument is currently experimental Starting second BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 22:18:41 CEST 2014 do_ypcall: clnt_call: RPC: Timed out Done BLAST searches. Starting ortholog detection... Output saved to file Output.int2.fasta-afum.fasta HTML output saved to orthologs.int2.fasta-afum.fasta.html Table output saved to table.int2.fasta-afum.fasta mysql output saved to sqltable.int2.fasta-afum.fasta sam28 at wbbi180:~/opt/inparanoid/int2_afum$ 2014-09-18 10:24 GMT+02:00 Erik Sonnhammer : > Hi, probably something went wrong with Blast. > > In the beginning of the output file Output.xxx you can see how many > homologs were detected by Blast, that will probably tell you what went > wrong. > > Erik Sonnhammer > > > On 09/18/2014 03:19 AM, Sammy Desilva wrote: > > Hello, > > I downloaded the latest version of Inparanoid8 on my Ubuntu 12.1 > and ran Inparanoid on 2 big proteome. On the default paramete the > algorithm resulted only 70 groups while when I used orthomcl on same > dataset it resulted around 3000 groups. > Please let me know what i am doing wrong? > > Thanks > Sam > > > _______________________________________________ > 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 sammy.ich17 at gmail.com Fri Sep 19 13:32:45 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Fri, 19 Sep 2014 13:32:45 +0200 Subject: [Inparanoid] Problem with Inparanoid groups In-Reply-To: <541AA1FC.4040908@scilifelab.se> References: <541A96D1.4010505@scilifelab.se> <541AA1FC.4040908@scilifelab.se> Message-ID: I got the error.. It was do_ypcall: clnt_call:RPC: Timed out 2014-09-18 11:12 GMT+02:00 Erik Sonnhammer : > Well clearly you can't expect more than 71 orthologs if that's how many > homologs Blast finds. > > My guess is that your sequences are not read properly by Blast. > > Erik > > > On 09/18/2014 10:45 AM, Sammy Desilva wrote: > > This is my truncated output: > > 18651 sequences in file int1.fasta > 9630 sequences in file afum.fasta > 143 sequences int1.fasta have homologs in dataset afum.fasta > 71 sequences afum.fasta have homologs in dataset int1.fasta > 184 int1.fasta-int1.fasta matches > 101 afum.fasta-afum.fasta matches > ################################### > 66 groups of orthologs > 87 in-paralogs from int1.fasta > 77 in-paralogs from afum.fasta > Grey zone 0 bits > Score cutoff 40 bits > In-paralogs with confidence less than 0.05 not shown > Sequence overlap cutoff 0.5 > Group merging cutoff 0.5 > Scoring matrix BLOSUM62 > ################################### > > ___________________________________________________________________________________ > Group of orthologs #1. Best score 122 bits > Score difference with first non-orthologous sequence - int1.fasta:3 > afum.fasta:122 > int1|P04914 100.00% afum|XP_752748.1 100.00% > afum|XP_755719.2 85.71% > Bootstrap support for int1|P04914 as seed ortholog is 100%. > Bootstrap support for afum|XP_752748.1 as seed ortholog is 100%. > .. > Score difference with first non-orthologous sequence - int1.fasta:41 > afum.fasta:41 > int1|Q9VTE5 100.00% afum|XP_750133.1 100.00% > Bootstrap support for int1|Q9VTE5 as seed ortholog is 100%. > Bootstrap support for afum|XP_750133.1 as seed ortholog is 100%. > > This is the Screen LOG for other analysis with similar problem: > > sam28 at wbbi180:~/opt/inparanoid/int2_afum$ perl inparanoid.pl int2.fasta > afum.fasta > 18486 sequences in file int2.fasta > 9096 sequences in file afum.fasta > Trying to run BLAST now - this may take several hours ... or days in worst > case! > Formatting BLAST databases > Done formatting > Starting BLAST searches... > > Starting first BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 > 18:12:38 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > > > Starting second BLAST pass for int2.fasta - int2.fasta on Wed Sep 17 > 20:05:44 CEST 2014 > do_ypcall: clnt_call: RPC: Timed out > > Starting first BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 > 20:22:59 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > > Starting second BLAST pass for int2.fasta - afum.fasta on Wed Sep 17 > 21:03:38 CEST 2014 > > Starting first BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 > 21:11:10 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > Selenocysteine (U) at position 37 replaced by X > > Starting second BLAST pass for afum.fasta - int2.fasta on Wed Sep 17 > 21:52:14 CEST 2014 > > Starting first BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 > 21:56:03 CEST 2014 > [blastall] WARNING: the -C 3 argument is currently experimental > > > Starting second BLAST pass for afum.fasta - afum.fasta on Wed Sep 17 > 22:18:41 CEST 2014 > do_ypcall: clnt_call: RPC: Timed out > Done BLAST searches. Starting ortholog detection... > Output saved to file Output.int2.fasta-afum.fasta > HTML output saved to orthologs.int2.fasta-afum.fasta.html > Table output saved to table.int2.fasta-afum.fasta > mysql output saved to sqltable.int2.fasta-afum.fasta > sam28 at wbbi180:~/opt/inparanoid/int2_afum$ > > > 2014-09-18 10:24 GMT+02:00 Erik Sonnhammer > : > >> Hi, probably something went wrong with Blast. >> >> In the beginning of the output file Output.xxx you can see how many >> homologs were detected by Blast, that will probably tell you what went >> wrong. >> >> Erik Sonnhammer >> >> >> On 09/18/2014 03:19 AM, Sammy Desilva wrote: >> >> Hello, >> >> I downloaded the latest version of Inparanoid8 on my Ubuntu 12.1 >> and ran Inparanoid on 2 big proteome. On the default paramete the >> algorithm resulted only 70 groups while when I used orthomcl on same >> dataset it resulted around 3000 groups. >> Please let me know what i am doing wrong? >> >> Thanks >> Sam >> >> >> _______________________________________________ >> 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 sammy.ich17 at gmail.com Fri Sep 19 13:40:10 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Fri, 19 Sep 2014 13:40:10 +0200 Subject: [Inparanoid] Analyzing multiple proteomes with Inparanoid Message-ID: 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? -------------- next part -------------- An HTML attachment was scrubbed... URL: From sammy.ich17 at gmail.com Sat Sep 20 11:32:15 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Sat, 20 Sep 2014 11:32:15 +0200 Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid Message-ID: 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: From sammy.ich17 at gmail.com Mon Sep 22 11:45:50 2014 From: sammy.ich17 at gmail.com (Sammy Desilva) Date: Mon, 22 Sep 2014 11:45:50 +0200 Subject: [Inparanoid] Performance of Inparanoid and blastall Warning Message-ID: Hi I am doing two species clustering. In compare to OrthoMcl , the Inparanod gives very few (5 time less ) clusters. What may be the problem? Job executed on Ubuntu but I also Got a Warning message [blastall] WARNING: the -C 3 argument is currently experimental Please Help Me. Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Mon Sep 22 14:33:05 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 22 Sep 2014 14:33:05 +0200 Subject: [Inparanoid] Analyzing 17 proteome orthology with Inparanoid In-Reply-To: References: Message-ID: <54201701.2050607@scilifelab.se> 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 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 erik.sonnhammer at scilifelab.se Mon Sep 22 14:34:10 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 22 Sep 2014 14:34:10 +0200 Subject: [Inparanoid] Performance of Inparanoid and blastall Warning In-Reply-To: References: Message-ID: <54201742.1050200@scilifelab.se> Hi, same answer as before - probably something goes wrong with Blast. Please check how many homologs are found, that will give a good idea if Blast worked or not. Erik Sonnhammer On 09/22/2014 11:45 AM, Sammy Desilva wrote: > Hi I am doing two species clustering. In compare to OrthoMcl , the > Inparanod gives very few (5 time less ) clusters. What may be the > problem? Job executed on Ubuntu but I also Got a Warning message > > [blastall] WARNING: the -C 3 argument is currently experimental > > > Please Help Me. Thanks > > > _______________________________________________ > 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: