[Biojava-l] ProteinTools

[Schreiber, Mark]

Hi -

I have corrected the naming of the method in the CVS. It looks like
someone did a copy and paste and forgot to rename the method. Everything
else about it seems OK.

As to point2. Probably Thomas is the best person to deal with the
interactions between biojava and BioSQL. My suggestion on this would be
that the method that puts the sequence into biosql doesn't call the
getName method on the alphabet but rather puts in "protein" or something
valid.

Another bigger issue is that a protein sequence (of the type you'd put
in a DB) doesn't really have termination residues. I understand that the
ProteinTAlphabet exists for translation purposes so you can make fancy
six frame translations of a DNA seq in which case you need the
termination symbols. Possibly splitting hairs here, what do others
think?

- Mark


> -----Original Message-----
> From: Mayank Thanawala [mailto:mthanawala@diadexus.com] 
> Sent: Thursday, 26 September 2002 4:52 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] ProteinTools
> 
> 
> Hi,
> 
> I was trying to create a protein sequence using ProteinTools; 
> I've found a couple of oddities:
> 
> 1.  There's a method called createDNASequence(..) [yes, in 
> ProteinTools] that claims to create a new Protein sequence 
> based on the input parameters.  Is this just a typo, or am I 
> missing something?
> 
> 2.  createProtein(seqstring) returns a SymbolList based on an 
> alphabet called PROTEIN-TERM (which is apparently a protein 
> alphabet with terminator characters permitted).  When you 
> call getName() on this alphabet, it returns "PROTEIN-TERM", 
> which is what BioSQLSequenceDB attempts to store in the 
> Molecule field of the Biosequence table when storing a 
> Sequence.  The problem is that that field is only 10 
> characters wide in the BioSQL spec, so when you do a
> BioSQLSequenceDB.addSequence(..) with the new sequence, it 
> fails.  I'm not really sure who's in charge of that schema, 
> but it'd be good if the default fields in Biojava were 
> friendly with the default spec for BioSQL...
> 
> Thanks!
> Mayank
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> 
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