[Biojava-l] Multiple Sequence Alignment with Profile HMMs

[mark.schreiber at novartis.com]

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" <ckol at iti.gr>
Sent by: biojava-l-bounces at lists.open-bio.org
09/05/2006 10:12 PM

 
        To:     <biojava-l at lists.open-bio.org>
        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


_______________________________________________
Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/biojava-l