Hello -
This example explains how you can do a pairwise alignment with a hidden
markov model. There is no specific implementation of a local alignment (eg
smith waterman). I've been thinking about it but I haven't gotten around
to it.
- Mark
"Christian Köberle" <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
08/18/2005 12:04 AM
To: biojava-l@biojava.org
cc: (bcc: Mark Schreiber/GP/Novartis)
Subject: [Biojava-l] RNA alignment
Hi,
1. is in bio-JAVA a implementation for local sequence alignment?
2. if yes, how can use this?
3. and how can i consider wobble-basepairs between the first
RNA-sequence and the reverse complement of the second RNA-sequence?
thanks
Christian
----------------------------------------
Christian Köberle
Max Planck Institut for Infection Biology
Department: Immunology
Schumannstr. 21/22
10117 Berlin
Tel: +49 30 28 460 562
e-mail: [EMAIL PROTECTED]
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