Hi all, Thank you all for the great suggestions. I've tried replacing the accension number and edited "taxon: " to "taxon:" MAUVE doesn't note that any error has occurred the annotations just don't show up. I would really like to see the annotations because I don't have a great reference (the best alignment I get is up to 27%). The MAUVE alignment visualizer simply says no annotations loaded. I hoped that being able to see the genes in my sequence I could better decide where that contigs need to go. I'm going to keep trying and see if I can get it to work or perhaps work around the problem. Again thank you all. ________________________________________ From: Aaron Darling [aaron.darl...@uts.edu.au] Sent: Monday, July 15, 2013 2:37 AM To: mauve-users@lists.sourceforge.net Subject: Re: [Mauve-users] (no subject)
Hi Simone, see below... On Fri, 2013-07-12 at 00:32 +0000, Bigelow, Simone wrote: > I have a draft genome which has been annotated using RAST but I cannot > get my RAST annotations to show up when using MAUVE to do an > alignment. The GenBank file created by RAST does not have an accession > number and simply calls it unknown and uses the contig id as the > locus. Is there any way to get my gbk file created using RAST to show > the annotations? It would help if you could copy, paste, and send any error messages produced by Mauve/BioJava in the Mauve Console window as it tries to load the alignment and annotations. In the past I have experienced problems with BioJava (which Mauve uses) loading RAST annotated genomes because RAST puts a space in the taxon db_xref line, e.g.: /db_xref="taxon: 6666666" Doing a search and replace of "taxon: " to "taxon:" in the .gbk file resolved the problem. I'm not sure if you're experiencing the same problem but it might be worth a try. Best, -Aaron -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users ------------------------------------------------------------------------------ See everything from the browser to the database with AppDynamics Get end-to-end visibility with application monitoring from AppDynamics Isolate bottlenecks and diagnose root cause in seconds. Start your free trial of AppDynamics Pro today! http://pubads.g.doubleclick.net/gampad/clk?id=48808831&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
