[Bioperl-l] RE: SeqIO fails on masked sequences

[Scott Markel]

PDB distibutes a FASTA file of the sequences associated with
the structures in the database.  The FASTA file contains both
nucleotides and proteins.  See pdb_seqres.txt in
ftp://ftp.rcsb.org/pub/pdb/derived_data/.

Scott

Wes Barris wrote:
> Hilmar Lapp wrote:
> 
>> You should not require by default that all sequences in one file be of 
>> the same type (alphabet). We never have required this, nor documented 
>> that it is a (not enforced) requirement, and so there may be people 
>> out there relying on this 'feature'.
> 
> 
> Mixing both DNA and protein sequences in one file and then attempting
> to process it seems like kind of a bizarre thing to want to do.  If
> the alphabet is explicitly specified, isn't there a way to make that
> take precedence?
> 
>>
>>     -hilmar
-- 
Scott Markel, Ph.D.
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