From erik.sonnhammer at scilifelab.se Wed Aug 20 16:45:46 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Wed, 20 Aug 2014 16:45:46 +0200 Subject: [Inparanoid] Result download failed - File not found In-Reply-To: <53BA8E6D020000EE0001C991@gwia2.boku.ac.at> References: <53BA8E6D020000EE0001C991@gwia2.boku.ac.at> Message-ID: <53F4B49A.30007@scilifelab.se> Dear Nadine, thanks for pointing this out. I guess you found the file you needed in the download directory, right? The links on the browse results page were broken because we had to change the way we store the InParanoid results, which are now over a hundred thousand files. The XML output link is fixed and still goes directly to the whole-proteome XML file, but the other formats are combined in a tar file, which is now linked to instead. I hope this is good enough. I hope I have not broken anything else by renaming the download directories to more informative names (a note to other users). Best wishes Erik Sonnhammer On 07/07/2014 12:11 PM, Nadine Elpida Tatto wrote: > Dear Sir or Madam, > > I've browsed through some datasets of your webservice InParnoid 8 and > tried to download/save the results in the three available formats. But > for each format I've got an error message (e.g. The requested URL > /download/current/table_stats/InParanoid.C.griseus-K.pastoris was not > found on this server.). > > Could you please help me with this issue? > > Thank you very much in advance > > Best Regards, > > Nadine Tatto > > > _______________________________________________ > 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 kmzhao at ou.edu Tue Aug 19 16:44:43 2014 From: kmzhao at ou.edu (Zhao, Kangmei) Date: Tue, 19 Aug 2014 14:44:43 +0000 Subject: [Inparanoid] ID Convert Message-ID: <18428B181D7E2348957BB1545829F8C20104CEEB90@it-lightning.sooner.net.ou.edu> Hello, I appreciate that you provide the file for the genome-scale pairwise orthologous relationship. Now I am working on a project related to the homology between rice and brachypodium. It seems that all of your files are using UniProt ID, however, my analysis is using gene locus ID. Since you have the tool of "gene search? on your website, is it possible if you could also provide the ?key? for UniProt? locus ID convert? It would be much easier for me to compare your result with my analysis. Appreciate your consideration of my request. Thank you very much! Best wishes, Kangmei Kangmei Zhao Graduate Student Department of Microbiology&Plant Biology University of Oklahoma 770 Van Vleet Oval Norman, OK 73019 -------------- next part -------------- An HTML attachment was scrubbed... URL: From som.anup at gmail.com Mon Aug 25 08:26:55 2014 From: som.anup at gmail.com (Anup Som) Date: Mon, 25 Aug 2014 11:56:55 +0530 Subject: [Inparanoid] Fwd: Query (Orthologs between Chicken and C. Elegans) In-Reply-To: References: Message-ID: I was using In-Paranoid database for retrieving the all orthologs between Chicken and C. Elegans where it shows there are 4154 orthologs between them. Interestingly For the same query Ensembl database gives more than 6000 orthologs between Chicken and C. Elegans. I am wondering why the significant difference results produced by the two robust databases. I am awaiting for your reply. Thanks & regards, Dr. Anup Som University of Allahabad Allahabad - 211002, INDIA -- ========== Dr. Anup Som Assistant Professor Center of Bioinformatics Institute of Interdisciplinary Studies Faculty of Science University of Allahabad Allahabad - 211002, INDIA Email: som.anup at gmail.com asom at allduniv.ac.in -------------- next part -------------- An HTML attachment was scrubbed... URL: From erik.sonnhammer at scilifelab.se Mon Aug 25 16:32:07 2014 From: erik.sonnhammer at scilifelab.se (Erik Sonnhammer) Date: Mon, 25 Aug 2014 16:32:07 +0200 Subject: [Inparanoid] Fwd: Query (Orthologs between Chicken and C. Elegans) In-Reply-To: References: Message-ID: <53FB48E7.1010704@scilifelab.se> Hi Anup, There are 4154 */ortholog groups/* between chicken and worm in InParanoid 8. But these groups contain 6264 chicken and 5135 worm proteins, as sometimes there are multiple inparalogs in an ortholog group. Note that we limit the dataset to 1 protein per gene (normally the longest). I hope this helps. Erik Sonnhammer On 08/25/2014 08:26 AM, Anup Som wrote: > > > I was using In-Paranoid database for retrieving the all orthologs > between Chicken and C. Elegans where it shows there are 4154 > orthologs between them. Interestingly For the same query Ensembl > database gives more than 6000 orthologs between Chicken and C. > Elegans. I am wondering why the significant difference results > produced by the two robust databases. > > I am awaiting for your reply. > > Thanks & regards, > Dr. Anup Som > University of Allahabad > Allahabad - 211002, INDIA > > > > > -- > ========== > Dr. Anup Som > Assistant Professor > Center of Bioinformatics > Institute of Interdisciplinary Studies > Faculty of Science > University of Allahabad > Allahabad - 211002, INDIA > Email: som.anup at gmail.com > asom at allduniv.ac.in > > > _______________________________________________ > 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: