[EMBOSS] showfeat: joining compound features
mthon at tamu.edu
Thu Sep 21 14:04:02 UTC 2006
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.
On Sep 19, 2006, at 10:08 AM, Thomas Girke wrote:
> If you know R a little bit then you may want to try this R script.
> 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:
> 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.
>> EMBOSS mailing list
>> EMBOSS at lists.open-bio.org
> Thomas Girke, Ph.D.
> 1008 Noel T. Keen Hall
> Center for Plant Cell Biology (CEPCEB)
> University of California
> Riverside, CA 92521
> E-mail: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
> Ph: 951-827-2469
> Fax: 951-827-4437
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