[Bioperl-l] Extracting a particular feature from a sequence

[Marc Logghe]

> :-) Yes I am using extractfeat, and maybe you can help - the 
> information I really need for this CDS is what STRAND it is 
> on.  As you will know, extractfeat extracts the sequence in 
> the direction that the feature runs, so if it is on the -1 
> strand, the feature sequence runs in the opposite direction 
> to a feature on the +1 strand.  I just need to know
> *when* extractfeat has done that, but no matter how hard I 
> look, I can't find anywhere that extractfeat can put that 
> information....?
Hi Mick,
Nope, don't find that neither.
Another route you could follow: convert your genbank feature table into
gff (bp_genbank2gff.pl or bp_genbank2gff3.pl, or even using EMBOSS:
seqret your.gb  -feature -offormat2 gff).
Next, using the in memory adaptor of gbrowse you can perfectly query
this gff "database" for the features you'd like and get hands on the
strand information.
I'll try to dig up an example script and come back to you.
Cheers,
Marc