Comments for Dr Motifs - Blog http://drmotifs.genouest.org Pattern matching and discovery in bioinformatics Fri, 30 Mar 2012 07:17:27 +0000 hourly 1 http://wordpress.org/?v=3.3.1 Comment on Blast+ web interface: source code available by A. Bretaudeau http://drmotifs.genouest.org/2011/09/blast-web-interface-source-code-available/comment-page-1/#comment-2634 A. Bretaudeau Fri, 30 Mar 2012 07:17:27 +0000 http://drmotifs.genouest.org/?p=167#comment-2634 Hi, You get this error because 'git submodule add...' only works if your symfony project is managed with git. For more information on how to set up a git repository for a symfony project, have a look at the <a href="http://symfony.com/doc/current/cookbook/workflow/new_project_git.html" rel="nofollow">Symfony documentation</a>. If you don't want to manage your project with git, you can also use the 'deps' file as explained in the Symfony documentation, or use 'git clone' to download the bundle code. Tell me if you need more help! Hi,
You get this error because ‘git submodule add…’ only works if your symfony project is managed with git.
For more information on how to set up a git repository for a symfony project, have a look at the Symfony documentation.
If you don’t want to manage your project with git, you can also use the ‘deps’ file as explained in the Symfony documentation, or use ‘git clone’ to download the bundle code.
Tell me if you need more help!

]]> Comment on Blast+ web interface: source code available by Mahesh http://drmotifs.genouest.org/2011/09/blast-web-interface-source-code-available/comment-page-1/#comment-2616 Mahesh Thu, 29 Mar 2012 14:55:59 +0000 http://drmotifs.genouest.org/?p=167#comment-2616 Hi, I am trying to follow the guide to install this interface but when trying to install the GenouestBioinfoBundle using the instructions provided I encounter the following error "fatal: Not a git repository (or any parent up to mount parent /home)" Searching the web seems to suggest a corrupt repository... Can you help please as I would like to deploy this. Many Thanks Hi, I am trying to follow the guide to install this interface but when trying to install the GenouestBioinfoBundle using the instructions provided I encounter the following error “fatal: Not a git repository (or any parent up to mount parent /home)”

Searching the web seems to suggest a corrupt repository… Can you help please as I would like to deploy this.

Many Thanks

]]> Comment on How to use InterProScan by A. Bretaudeau http://drmotifs.genouest.org/2010/04/how-to-use-interproscan/comment-page-1/#comment-1781 A. Bretaudeau Mon, 19 Dec 2011 09:55:49 +0000 http://drmotifs.genouest.org/?p=30#comment-1781 IPR unintegrated means that InterProScan found a match on your sequence with a motif that doesn't have a corresponding InterPro ID. This motif is only available in the member database with the given specific ID. IPR unintegrated means that InterProScan found a match on your sequence with a motif that doesn’t have a corresponding InterPro ID. This motif is only available in the member database with the given specific ID.

]]> Comment on How to use InterProScan by shefali http://drmotifs.genouest.org/2010/04/how-to-use-interproscan/comment-page-1/#comment-1780 shefali Mon, 19 Dec 2011 09:40:53 +0000 http://drmotifs.genouest.org/?p=30#comment-1780 i have a query regarding interproscan results?? what IPR unintegrated term represent in results ?waiting for quick response .. i have a query regarding interproscan results?? what IPR unintegrated term represent in results ?waiting for quick response ..

]]> Comment on MEME 4.6: MEME-ChIP and Spamo by A. Bretaudeau http://drmotifs.genouest.org/2011/02/meme-4-6-meme-chip-and-spamo/comment-page-1/#comment-1294 A. Bretaudeau Tue, 07 Jun 2011 07:38:55 +0000 http://drmotifs.genouest.org/?p=149#comment-1294 Hi, This could be a bug in spamo. I think the best is to contact the authors of meme and see if they can find a solution. Their address is meme@nbcr.net Hi,
This could be a bug in spamo. I think the best is to contact the authors of meme and see if they can find a solution. Their address is meme@nbcr.net

]]> Comment on MEME 4.6: MEME-ChIP and Spamo by Prashant Srivastava http://drmotifs.genouest.org/2011/02/meme-4-6-meme-chip-and-spamo/comment-page-1/#comment-1291 Prashant Srivastava Mon, 06 Jun 2011 17:32:45 +0000 http://drmotifs.genouest.org/?p=149#comment-1291 I am currently using Spamo for analysing ~9,000 short sequences (100-200 bp) with transfac matrices ... if I try to run the program under high stingency condition i.e. p value < 10e-6 program works but as soon as I go with the default parameters it gives segmentation error. Can you please comment/suggest on this I am currently using Spamo for analysing ~9,000 short sequences (100-200 bp) with transfac matrices … if I try to run the program under high stingency condition i.e. p value < 10e-6 program works but as soon as I go with the default parameters it gives segmentation error. Can you please comment/suggest on this

]]> Comment on Hiden Markov Models (HMM) by The technical architecture | Dr Motifs – Blog http://drmotifs.genouest.org/2010/07/hiden-markov-models-hmm/comment-page-1/#comment-1265 The technical architecture | Dr Motifs – Blog Thu, 26 May 2011 12:03:13 +0000 http://drmotifs.genouest.org/?p=58#comment-1265 [...] to create a multiple alignment using clustalw, then directly use this alignement to construct an HMM with hmmbuild and finally use this HMM to search within a database for similar sequences using [...] [...] to create a multiple alignment using clustalw, then directly use this alignement to construct an HMM with hmmbuild and finally use this HMM to search within a database for similar sequences using [...]

]]> Comment on How to use InterProScan by InterProScan: new web form and web service | Dr Motifs – Blog http://drmotifs.genouest.org/2010/04/how-to-use-interproscan/comment-page-1/#comment-1264 InterProScan: new web form and web service | Dr Motifs – Blog Thu, 26 May 2011 12:00:56 +0000 http://drmotifs.genouest.org/?p=30#comment-1264 [...] Remember the InterProScan how-to? [...] [...] Remember the InterProScan how-to? [...]

]]> Comment on MEME overview by Blast+ and MEME updates | Dr Motifs – Blog http://drmotifs.genouest.org/2011/01/meme-overview/comment-page-1/#comment-1119 Blast+ and MEME updates | Dr Motifs – Blog Tue, 05 Apr 2011 09:57:31 +0000 http://drmotifs.genouest.org/?p=136#comment-1119 [...] is now available from the command line. It may be useful if you want to test it on our cluster: see this post if you don’t know how to use it from command [...] [...] is now available from the command line. It may be useful if you want to test it on our cluster: see this post if you don’t know how to use it from command [...]

]]> Comment on New BLAST+ web form by Alan http://drmotifs.genouest.org/2011/02/new-blast-web-form/comment-page-1/#comment-1089 Alan Fri, 25 Mar 2011 12:40:47 +0000 http://drmotifs.genouest.org/?p=141#comment-1089 Yeah, for those of us who do in-house BLAST. Your form is much better than wwwblast! Yeah, for those of us who do in-house BLAST. Your form is much better than wwwblast!

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