[EMBOSS] showfeat: joining compound features

[Michael Thon]

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
>>
>>
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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: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
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