From hickt at smail.uni-koeln.de Wed May 6 15:38:00 2015 From: hickt at smail.uni-koeln.de (Timon Hick) Date: Wed, 06 May 2015 15:38:00 +0200 Subject: [Inparanoid] InParanoid 4.1 Message-ID: <554A1938.5060809@smail.uni-koeln.de> Dear InParanoid-Mailinglist, I am currently working on a project for which I need a bunch of orthology information and I found your database/program to fit my needs. In order to elucidate whether I should use the orthology data available in the download section of your website or whether I should run the program locally, some questions occured, which I wanted to post here, hoping to get professional advice. I subscribed for the standalone version 4.1 of InParanoid and ran it (without changes in the script) on two sequence files, which I also got from your website (v. 8.0, processed). I also loaded the respective archive from your website and compared the sql-tables from both outputs. As far as I am informed, the othology data available on your website were obtained using the same version as me, so I thought the results should be the same, but they were not. So my question is, if you know, where these differences could come from. Another question is, whether the intermediate files (BLAST-outputs) of the runs from which the online available results came from, are available too. I really hope to get help from you and thank you in advance for every answer. Best Wishes Timon From erik.sonnhammer at scilifelab.se Fri May 8 10:11:42 2015 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Fri, 08 May 2015 10:11:42 +0200 Subject: [Inparanoid] InParanoid 4.1 In-Reply-To: <554C6BB8.3030406@smail.uni-koeln.de> References: <554A1938.5060809@smail.uni-koeln.de> <554A3238.6040800@scilifelab.se> <554B260B.60703@smail.uni-koeln.de> <554B6266.4010600@scilifelab.se> <554C6BB8.3030406@smail.uni-koeln.de> Message-ID: <554C6FBE.9050306@scilifelab.se> Yes, I would think so. /Erik On 05/08/2015 09:54 AM, Timon Hick wrote: > Hi, > > tanks for your reply. I just checked the version of my blastall and its > 2.2.26. So I assume, that the differences can be considered as "normal", > right? > > Best Wishes > > Timon > > On 07.05.2015 15:02, Erik Sonnhammer wrote: >> Hi, >> >> These are not huge differences; this can happen if many homologs are >> border-line (near 40 bits in score). I think we have seen such >> differences between Blast versions - we used blastall 2.2.18. If you are >> also using that, then I admit it is a bit strange. >> >> /Erik >> >> On 2015-05-07 10:44, Timon Hick wrote: >>> Dear Erik, >>> >>> thank you for your very fast response. >>> Some of the differences were indeed very small, like scores differing >>> 1 percent, but I already thought that to be no major problem. >>> >>> I have just performed another run of InParanoid on B. bovis against M. >>> tuberculosis and obtained yet another result, which is still different >>> to the one, from your website. In numbers: >>> >>> Server-Version: >>> 207 groups of orthologs >>> 241 in-paralogs from B. bovis >>> 275 in-paralogs from M. tuberculosis >>> >>> local version: >>> 204 groups of orthologs >>> 235 in-paralogs from B. bovis >>> 268 in-paralogs from M. tuberculosis >>> >>> In a previous run, there were less than 200 groups of orthologs. >>> >>> What is the reason, that every run yields a different result? >>> >>> And are these differences to be considered as big? >>> >>> If you need further information to find the problem, let me know. >>> >>> Thank you again for your response and your help. >>> >>> Timon Hick >>> >>> Am 06.05.2015 um 17:24 schrieb Erik Sonnhammer: >>>> Dear Timon, >>>> >>>> there can be small differences between the on-line and regenerated >>>> InParanoid orthologs, but if there are big ones then probably something >>>> went wrong. >>>> >>>> Small differences may come from different blast versions, differences in >>>> the InParanoid script that we ran (a speed-optimised version for compute >>>> clusters), and arithmetic differences between operating systems. >>>> >>>> We have archived the blast outputs but it would be a lot of work to dig >>>> them up. >>>> >>>> In terms of nr of orthologs, how different are the results? >>>> >>>> Erik Sonnhammer >>>> >>>> On 2015-05-06 15:38, Timon Hick wrote: >>>>> Dear InParanoid-Mailinglist, >>>>> >>>>> I am currently working on a project for which I need a bunch of >>>>> orthology information and I found your database/program to fit my >>>>> needs. >>>>> In order to elucidate whether I should use the orthology data available >>>>> in the download section of your website or whether I should run the >>>>> program locally, some questions occured, which I wanted to post here, >>>>> hoping to get professional advice. >>>>> >>>>> I subscribed for the standalone version 4.1 of InParanoid and ran it >>>>> (without changes in the script) on two sequence files, which I also got >>>>> from your website (v. 8.0, processed). I also loaded the respective >>>>> archive from your website and compared the sql-tables from both >>>>> outputs. >>>>> >>>>> As far as I am informed, the othology data available on your website >>>>> were obtained using the same version as me, so I thought the results >>>>> should be the same, but they were not. >>>>> >>>>> So my question is, if you know, where these differences could come >>>>> from. >>>>> >>>>> Another question is, whether the intermediate files (BLAST-outputs) of >>>>> the runs from which the online available results came from, are >>>>> available too. >>>>> >>>>> I really hope to get help from you and thank you in advance for every >>>>> answer. >>>>> >>>>> Best Wishes >>>>> >>>>> Timon >>>>> _______________________________________________ >>>>> InParanoid mailing list >>>>> InParanoid at lists.su.se >>>>> https://lists.su.se/mailman/listinfo/inparanoid-at-sbc.su.se From sanae.el-mhijar at etu.univ-nantes.fr Sun May 31 14:33:03 2015 From: sanae.el-mhijar at etu.univ-nantes.fr (EL MHIJAR Sanae) Date: Sun, 31 May 2015 14:33:03 +0200 Subject: [Inparanoid] Question Message-ID: <556AFF7F.4050109@etu.univ-nantes.fr> Dear InParanoid-Mailinglist, I am working on a project and i use your database/program that it really help me. So i have one question about the score in this program , by default it's 40 bits, i dont understant why you choose 40 bits, and for cherche orthologues how we can choose this score please ? thank you in advance for every answer. Sanae