Hi, if your data are in gff format you could also try gff2ps: http://www1.imim.es/software/gfftools/GFF2PS.html Within EMBOSS there is also an application lindna but it has its own input format so you must first convert your gff file to lindna input.
HTH, David. [EMAIL PROTECTED] schrieb am 19/09/2006 17:08:44: > 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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
