[EMBOSS] showfeat: joining compound features

[Thomas Girke]

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.
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Center for Plant Cell Biology (CEPCEB)
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