Hi Shlomo, The Mauve Contig Mover is not able to reorder genbank annotations. If you would like to have a file with genbank format annotations on ordered contigs I would suggest ordering your contigs immediately after assembly then uploading to RAST for annotation. You can then calculate a new genome alignment on the ordered, annotated contigs if you so wish.
Best, -Aaron ________________________________________ From: Shlomo Blum [shlomo.b...@mail.huji.ac.il] Sent: Thursday, September 11, 2014 3:55 AM To: Aaron Darling Cc: mauve-users@lists.sourceforge.net Subject: Re: [Mauve-users] Annotations and Contigs Greetings, I'll join this email because I think I have a similar problem. I'm using MAUVE to reorder contigs. I used genbank files from RAST. In the first iteration, I can see the annotation all right. There is a copy of the original genbank file in this folder by the way. But in the next iterations the annotations disappear, the CDs are there, but all I get is a small box with "asap" and coordinates (?) in it, no "product" etc. I cleaned the cache, and now even the CDs are gone! In the end I would like to get a genbank file with the contigs in the correct order. I see that MAUVE returns a fasta file only with the contig sequences. Best regards, Shlomo On Wed, Sep 3, 2014 at 8:14 AM, Aaron Darling <aaron.darl...@uts.edu.au<mailto:aaron.darl...@uts.edu.au>> wrote: Hi Stephanie, In regard to your first question, it's not obvious why the alignment would open the first time with annotations but would fail in subsequent opens. Can you send a copy & paste of any messages in the console log window please? Another thing that might be worth trying would be to clear the alignment cache and then try opening again. To do so, select "Help"->"Clear alignment cache" from the menu. Best, -Aaron On Wed, 2014-09-03 at 05:58 +1000, Stephanie S Momeni wrote: > Greetings, > > > I am new to Mauve and comparative genomics in general. I ran 10 > genomes with annotations (genBank files) with Progressive Mauve. It > appears to work fine. However, once I close the alignment and try to > reopen, it loses all the annotations. Can someone please tell me how > to reopen the complete alignment with annotations so I don't have to > rerun it every time I want to do analysis. > > > Also, my genomes are assembled from contigs (about 400 per genome). > Since Mauve concatenates these, is there any way to know where one > contig ends and the next begins? > > > Any help with this is greatly appreciated. > > > Cheers > Stephanie -- 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. ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net<mailto:Mauve-users@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/mauve-users -- Dr. Shlomo Blum, DVM MSc Dept. of Bacteriology and Mycology Kimron Veterinary Institute POB 12 Bet Dagan, 50250 Israel Tel.: +972-3-9681680 Mob.: +972-50-6241862 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. ------------------------------------------------------------------------------ Want excitement? Manually upgrade your production database. When you want reliability, choose Perforce Perforce version control. Predictably reliable. http://pubads.g.doubleclick.net/gampad/clk?id=157508191&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
