[Bioperl-l] strange problem about seq->alphabet

Marc Logghe Marc.Logghe at DEVGEN.com
Wed Oct 12 09:48:30 EDT 2005

> i have some problem on extracting info. about seq->alphabet 
> from gb file.Because some sequences are mRNA while others are 
> DNA, but after running the code. it ignores mRNA but report 
> all are DNA. why it happen and how to solve it? 
You need to call $seq->molecule instead.
A call to alphabet will return the sequence alphabet, the valid types
being 'dna', 'rna' and 'protein'.
In case the sequence of the genbank record actually contains Us instead
of Ts, then alphabet *should* return 'rna'.
Molecule returns the molecule property extracted from the genbank LOCUS

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