Some examples are at: http://www.biojava.org/docs/bj_in_anger/profileHMM.htm
and http://www.biojava.org/tutorials/dp-doc.html Rahul Karnik <[EMAIL PROTECTED]> Sent by: [EMAIL PROTECTED] 09/20/2004 03:40 AM To: [EMAIL PROTECTED] cc: (bcc: Mark Schreiber/GP/Novartis) Subject: [Biojava-l] Per-sequence information from PairwiseAlignment Hello, [I am a new user of BioJava, so please forgive any obvious errors I may make.] I was trying to modify the PairwiseAlignment demo to show the traditional output of alignment programs, i.e. the aligned sequences alongside one another. It seems this information is available from: StatePath result = aligner.viterbi(seqs, ScoreType.PROBABILITY); I was able to get result.symbolListForLabel(StatePath.SEQUENCE) and display the symbols, but these seem to have both sequences in each symbol (of class SimpleAtomicSymbol). I could parse out each sequence from the combined SymbolList, but I was wondering if there is a better way to achieve this. Thanks, Rahul _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
