[EMBOSS] showfeat: joining compound features

Michael Thon mthon at tamu.edu
Tue Sep 19 14:27:44 UTC 2006


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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