Hi Stephanie,
The vertical red lines in each genome's "track" delineate the ends of
contigs (or, more precisely, separate fasta entries). If you click through
"File --> Open alignment" (I think these are the menu headings), and point
Mauve at the alignment file in the largest numbered directory (say, if
Mauve required 11 stages to converge, you should have an "alignment10"
folder with an "alignment10" file in it, perhaps), you'll open up that
previous alignment.
By the way, are you using Mauve's "contig reorder" tool (Move contigs in
the menu) to swap the order and orientation of assembled contigs, all with
respect to the best assembled genome? This should help clear up a lot of
crossing alignment blocks, if that's what you're seeing.
Hope that helped,
~Joe
On Tue, Sep 2, 2014 at 12:58 PM, Stephanie S Momeni <s...@uab.edu> 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
>
>
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--
Joseph Fass
Lead Data Analyst
UC Davis Genome Center - Bioinformatics Core
http://bioinformatics.ucdavis.edu/
jnf...@ucdavis.edu
phone ~ 530.752.2698
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