[Biojava-l] 3 questions and problems

["Andreas Dräger"]

Hello,

I would like to ask three questions or to mention problems, respectively.

1. Trying to write a protein-sequence in a GenPept file resulted in the  
following error message: ClassCastException in GenpeptFileFormer line 361.
What does this mean and how can I write my sequences?

2. There is a problem with BioSQL. The attribute alphabet in the table
biosequence has the type VARCHAR(10). The BioJava alphabet PROTEIN-TERM has
12 characters. I always got an error message, when I tryed to get a protein
sequence with this alphabet from the database. A simple select statement
showed that the alphabet in the table is abbrevated to PROTEIN-TE, which is
not equal to the BioJava name and causes trouble. I solved this problem by
altering the table declaration to VARCHAR(12). Now it works fine. Is there
another solution for this or should this be the only one?

3. I also experimented with the HMM for pair wise sequence alignments, which
was proposed in the cookbook. Has anybody an idea how one could combine this
HMM with the SubstitutionMatrix from the alignment package? I don't see how
we can produce a senseful distribution including a substitution matrix in
the match state. This might especially be hard to realize because we can't
exclude that there are some ambigious symbols in the sequences to be
aligned, which are not in the substitution matrix at all. I am thankfull for
any good ideas.


Sincerely
Andreas Dräger

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