Hi Thomas - Thanks for the script, I'm going to try it out. My need the other day was for an easy way to display features that I could show to my class. Showfeat ended up working alright so that's what we're using at the moment. gff2ps is also good at making graphics but I thought there should be an emboss way to do it too. cheers Mike
On Sep 19, 2006, at 10:08 AM, Thomas Girke wrote: > Micheal, > > If you know R a little bit then you may want to try this R script. > http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/My_R_Scripts/ > featureMap.txt > > I often use this script for plotting position information of all > kinds of EMBOSS > programs onto genes and chromosomes. > > To demo the utility of the script, simply paste this command into > the R console: > source("http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/ > My_R_Scripts/featureMap.txt") > > Best, > Thomas > > On Tue 09/19/06 09:27, Michael Thon wrote: >> Hello everyone - I am using showfeat to display blast similarity >> features that are stored in a gff file. From the documentation, it >> looks like showfeat can display multiple exon features on the same >> line but can it also do this with similarity features? Here is an >> example from my gff file: >> >> Chr5:4535154,4542653 BLAST similarity 2475 >> 5120 . . . Target "ref|XP_468448.1|" >> Chr5:4535154,4542653 BLAST similarity 3142 3480 >> 388 + . Target "ref|XP_468448.1|" 141 225 >> Chr5:4535154,4542653 BLAST similarity 4944 5120 >> 304 + . Target "ref|XP_468448.1|" 248 306 >> Chr5:4535154,4542653 BLAST similarity 2475 2603 >> 216 + . Target "ref|XP_468448.1|" 66 108 >> Chr5:4535154,4542653 BLAST similarity 2916 3017 >> 182 + . Target "ref|XP_468448.1|" 107 140 >> >> Also, is there an emboss program that does showfeat's functions but >> with a graphical, publication quality output? I am thinking of a >> graphic with colored feature tracks, etc. >> Thanks >> Mike >> >> >> _______________________________________________ >> EMBOSS mailing list >> [email protected] >> http://lists.open-bio.org/mailman/listinfo/emboss >> > > -- > Thomas Girke, Ph.D. > 1008 Noel T. Keen Hall > Center for Plant Cell Biology (CEPCEB) > University of California > Riverside, CA 92521 > > E-mail: [EMAIL PROTECTED] > Website: http://faculty.ucr.edu/~tgirke > Ph: 951-827-2469 > Fax: 951-827-4437 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
