Hi -
At the moment the biojava HMMs can only do pairwise alignments. Your only
options would be to do multiple pairwise alignments (following the
principles of ClustalW) or align everything to a profile.
- Mark
Mark Schreiber
Research Investigator (Bioinformatics)
Novartis Institute for Tropical Diseases (NITD)
10 Biopolis Road
#05-01 Chromos
Singapore 138670
www.nitd.novartis.com
phone +65 6722 2973
fax +65 6722 2910
"Chrysa Collyda" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
09/05/2006 10:12 PM
To: <[email protected]>
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] Multiple Sequence Alignment with Profile
HMMs
Hello all,
I would like to pose again a question regarding multiple sequence
alignment with profile HMMs. Any help would be deeply appreciated.
i created a profile hmm from a set of unaligned homologues sequences then
i aligned some sequences to the model.i noticed that every sequence has
its own length for the alignment.is there any method by which i can create
a multiple sequence alignment between these sequences?
thanks in advance,
ckol
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