[EMBOSS] Dot Plot

[Guy Bottu]

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