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>
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
>
>
>
>
>
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--
*Dr. Shlomo Blum, DVM MSc*
*Dept. of Bacteriology and Mycology*
*Kimron Veterinary Institute*
*POB 12*
*Bet Dagan, 50250*
*Israel*
*Tel.: +972-3-9681680*
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