[EMBOSS] showfeat: joining compound features

[David.Bauer at SCHERING.DE]

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.

emboss-bounces at lists.open-bio.org 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
> >
> >
> > _______________________________________________
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> > EMBOSS at lists.open-bio.org
> > 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: thomas.girke at ucr.edu
> Website: http://faculty.ucr.edu/~tgirke
> Ph: 951-827-2469
> Fax: 951-827-4437
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