[Biojava-l] Per-sequence information from PairwiseAlignment

[mark.schreiber at group.novartis.com]

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 <rahul at genebrew.com>
Sent by: biojava-l-bounces at portal.open-bio.org
09/20/2004 03:40 AM

 
        To:     biojava-l at biojava.org
        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
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