[Bioperl-l] Sequences for joined features (in a Genbank file)

jchuang@ucsf-104-53.ucsf.edu jchuang@ucsf-104-53.ucsf.edu
Tue, 26 Feb 2002 19:17:08 -0800 (PST)


I'm trying to extract the DNA sequence from features of genbank files
(e.g. the CDS). The seq function does this great whenever I have a
contiguous sequence, but it doesn't appear to work properly when the
feature is made up of joined sequences.  Instead of a patching together of 
all the joined subsequences, I get the sequence starting with the first 
start site and ending with the last end site.

Is there a way to extract the patched together sequence instead? I 
couldn't tell from the docs if this feature had been implemented. The 
Location modules look relevant, but I didn't see a way to use them on 
sequence objects.

Thanks for any help.


Jeffrey Chuang
UC San Francisco - Dept. of Biochemistry and Biophysics
513 Parnassus Avenue
Box 0448
San Francisco, CA 94143-0001
W: 415-514-2616