Hi Robin,
Artemis is a good option as Alex suggests.
You could use any feature viewer available if you are just interested in
visualizing SNPs. It would be easy to convert the output of mummer's
"show-snps" tool into the input format required by these tools to view the
snps and indels with respect to the annotations.
Best,
-Adam
On Thu, May 6, 2010 at 4:16 PM, Bossers, Alex <Alex.Bossers@...> wrote:
> Robin,
> not sure whether you are exactly looking for this.... but we visualise all
> our (bacterial) genome MUMMER alignments in free Artemis Comparison Tool
> (java/webstart based tool from Sanger).
> http://www.sanger.ac.uk/resources/software/act/
> or the webstart:
> http://www.sanger.ac.uk/resources/software/act/java/act_current.jnlp
>
> Above the sequences you can easily read any embl or gff feature file to map
> differences to annotation.
>
> Cheers,
> Alex
>
> ________________________________
>
> Van: Robin Colgrove [mailto:robin@...]
> Verzonden: do 6-5-2010 17:55
> Aan: mummer-help@...
> Onderwerp: [MUMmer-help] Graphical displays using MUMMER
>
>
> Hello
>
> I have some ~100 kb viral genomes that I have sequenced, ~98% homologous,
> and I am trying to figure out how to display the alignments generated by
> MUMMER in some more informative fashion than the dotplot. For example, I
> would like to just show the distribution of all the SNP's and indels and
> mark which are in genes vs intragenic regions. I have to think there is a
> straightforward way to do this, but I can't figure it our from the manual.
>
> thanks for any leads, links, tutorials, etc!
>
> Robin Colgrove
> Harvard Medical School
> Dept of Microbiology
>
>
>
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