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
>
>
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>
--
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
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