[Biojava-l] ProteinTools

Mayank Thanawala mthanawala@diadexus.com
Wed, 25 Sep 2002 09:52:28 -0700


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