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" <[EMAIL PROTECTED]> 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 > > > _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
