[Bioperl-l] Re: predicted_cds method doesn't return a promaryseqI obj

[Hilmar Lapp]

Jason Stajich wrote:
> 
> Dan -
> 
> You're going to need to get the CDS from the gene object not the exon
> object - genscan doesn't provide the individual exon sequences, just the
> full CDS.  Even though the exon object has a predicted_cds it doesn't
> necessarily mean it is filled in (but it is for MZEF prediction parsing).

Correct. The reason MZEF is different is because it only predicts
(at least used to predict; not sure this is still true) exons,
not genes as a composition of exons.

>         Subject: predicted_cds method doesn't return a promaryseqI obj

In your example, it just returned undef.

	-hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
San Diego, Ca. 92130                     phone: +1 858 812 1757
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