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 -- Lust, ein paar Euro nebenbei zu verdienen? Ohne Kosten, ohne Risiko! Satte Provisionen für GMX Partner: http://www.gmx.net/de/go/partner _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
