Re: [MUMmer-help] Mapview Options

[Adam P. <aph...@gm...>]

Hi Martin,
Q1: I'm afraid the mapview script is in need of serious repair. It is likely
you are doing everything right and the script is simply broken. The
developer of that tool is no longer with our group and no one has had the
motivation to keep up with it. My apologies.

Q2: Not that I am aware of. You can have mapview output xfig files which can
be edited by hand if you know the language. Personally, I prefer dot plots
(e.g. mummerplot) over the linear plots, so those tools get more of my
development efforts. But with mummerplot you can't view the alignments in
the context of the annotation. I've been doing a little work on a
replacement for mummerplot that will include annotation info, but it's not
ready for release yet.

Your other option is to load mummer alignments and annotation info into a
generic feature browser like the USCS genome browser, or the Argo genome
browser. I've used CGView for circular chromosomes before and was pretty
happy with it (http://wishart.biology.ualberta.ca/cgview/). There are
probably many more of these types of tools available. Usually they just need
a start and end coordinate for the features, so it would be easy to reformat
the output of show-coords into what you need.

Good luck!
-Adam



On Fri, Feb 20, 2009 at 3:31 AM, Dr. Martin Selke <m....@gm...> wrote:

> Hello,
>
> thanks again for getting me started with MUMmer!
>
> I'm currently trying to optimize my "output-abilities", following the
> tutorials from the MUMmer page. Though I managed to successfully adapt the
> tutorials to my own workflow, I have problems adding more of the options for
> example when using mapview.
>
> QUESTION 1:
> I used the following line as the basis for the final coords-processing:
> mapview -n 1 -p 3_5_comparison 3_5.coords
>
> When I tried to add different program options from the list of the manual
> either I got a failure message or, and that's mostly the case, nothing
> happens/changes in the output fig.
>
> I would like to add the query and reference name to the graph using -I and
> -Ir. Why don't they appear, when I use the following command line:
> mapview -n 1 -p 3_5_comparison -I -Ir 3_5.coords?
>
> Adding a string behind the -I/-Ir tag like in the -p tag doesn't seem to be
> the answer.
>
> QUESTION 2:
> When comparing two different nucleotide sequences with a third one, is
> there a possibility to combine the mapview information in one graph? I did
> this by hand using the PDFs in Photoshop, altering the coloring by hand and
> making an overlay. It's doable and refreshing my graphic design hobby but a
> little time consuming. ;) Is there a MUMmer extension/spin-off which can by
> chance do an overlay of different comparisons automatically (or in another
> way) as one graphical output?
>
> Thanks in advance and happy MUMmering everybody! ;)
> Sincerly,
> Martin Selke
>
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> Dr. Martin Selke
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