[Bioperl-l] CDS is a complement

[Hilmar Lapp]

Malgorzata Kaminska wrote:
> 
> Hello everyone!
> 
>     This is perhaps a trivial matter, but would anyone know how I can
> determine if a CDS of interest is in fact a complement or not.  In other
> words, I have no problem in finding the CDS that interests me, or in using
> the revcom() method.  However, I am still unable to determine (other than
> actually going in and checking visually) if before the start and end of the
> nucleotide sequence range there is the word "complement" (i.e., the whole
> CDS line would then read "CDS     complement (46833..67464)".   Would anyone
> have any ideas/suggestions?

Assuming that you obtain the CDS from a Bioperl parse of some
feature table (most probably GenBank or EMBL-formatted sequence
records), you can ask the feature object representing the CDS for
the strand: $feat->strand(). This returns -1, 0, and 1, for minus,
unknown, and plus strand. complement would result in a minus
strand being assigned.

	Hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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