I could give it a try. But how do you think it would solve the problem? I
mean, the idea with Mauve is to align genomes and extract regions of
interest (either homologs or strain-specific). So the best would be to be
able to align genomes with Mauve and keep the annotations and thus extract
those regions already annotated for further analysis.
On Sun, Jul 14, 2013 at 8:41 PM, Bats <bdbel...@gmail.com> wrote:
> Have you considered running RAST after the contigs are reorder/aligned
> to your reference genome?
>
>
> On 7/13/2013 5:56 AM, Shlomo Blum wrote:
> > Actually it is the NCBI's PGAAP output file that had an empty "VERSION"
> > field. The RAST output works fine for me. However, I must say that when
> > I use the "reorder contigs" option, I "loose" the annotations after the
> > first iteration. The first alignment looks fine, but then, in the last
> > iteration, I got only a "asap" field in the annotation - when using the
> > RAST output.
> >
> >
> > On Fri, Jul 12, 2013 at 11:58 PM, Shlomo Blum
> > <shlomo.b...@mail.huji.ac.il <mailto:shlomo.b...@mail.huji.ac.il>>
> wrote:
> >
> > I had a similar problem. The RAST genbank file has an empty
> > "VERSION" entry. You can add "something" to this entry and if I
> > remember it right this made it work for me.
> >
> > Shlomo
> >
> >
> > On Fri, Jul 12, 2013 at 3:32 AM, Bigelow, Simone
> > <simone.bige...@okstate.edu <mailto:simone.bige...@okstate.edu>>
> 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?
> >
> >
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> >
> >
> >
> >
> > --
> > *Dr. Shlomo Blum*
> > *Dept. of Bacteriology*
> > *Kimron Veterinary Inst.*
> > *POB 12*
> > *Bet Dagan, 50250*
> > *Israel*
> > *Tel.: 972-3-9681680*
> >
> >
> >
> >
> > --
> > *Dr. Shlomo Blum*
> > *Dept. of Bacteriology*
> > *Kimron Veterinary Inst.*
> > *POB 12*
> > *Bet Dagan, 50250*
> > *Israel*
> > *Tel.: 972-3-9681680*
> >
> >
> >
> >
> ------------------------------------------------------------------------------
> > 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
> >
> >
> >
> > _______________________________________________
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> > Mauve-users@lists.sourceforge.net
> > https://lists.sourceforge.net/lists/listinfo/mauve-users
> >
>
--
*Dr. Shlomo Blum*
*Dept. of Bacteriology*
*Kimron Veterinary Inst.*
*POB 12*
*Bet Dagan, 50250*
*Israel*
*Tel.: 972-3-9681680*
------------------------------------------------------------------------------
See everything from the browser to the database with AppDynamics
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