[EMBOSS] Dot Plot

[Staffa, Nick (NIH/NIEHS)]

Thanks.
After a day of futzing around trying to create the point file that GCG's
Compare makes, with an whole page of Perl, I attacked the figure file it
makes. If one doesnt care about axes, then 2 or 3 commands set up the window
and one adds his points in the original units  ­ a half page of perl.
Figure is a great program. It's so old that surely they could open source
it.


On 5/29/08 5:53 AM, "Guy Bottu" <gbottu at vub.ac.be> wrote:

> Staffa, Nick (NIH/NIEHS) wrote:
>> I am doing a genomic survey of sorts.
>> I generate a lot of X,Y coordinates.
>> I would like to make a plot of these.
> 
> If you have still a copy of GCG lingering around : GCG has separate programs
> to 
> compute the XY-coordinates and actually draw the plot (dotplot). You will of
> course need to write a Perl script to put the coordinates in the format used
> by 
> dotplot.
> 
> Another possibility I can think about are tools created by the UCSC. If you
> can 
> get your coordinates in the right lav-like format (tricky, because it are not
> individual dots but rather stright line segments), you could use the LAJ Java
> application (interactive) or the mkdotplot program from the PipMaker server
> (creates PostScript file). You can look at
> http://oryx.ulb.ac.be/embosshelp/blastz.html#output
> to get a snapshot how the input ada.blastz and the output
> ada.blastz.dotplot.pdf
> look like.
> 
> Regards,
> Guy Bottu,
> Belgian EMBnet Node
> 
> 
>