[Biojava-l] RNA alignment

mark.schreiber at novartis.com mark.schreiber at novartis.com
Wed Aug 17 21:42:46 EDT 2005

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" <koeberle at mpiib-berlin.mpg.de>
Sent by: biojava-l-bounces at portal.open-bio.org
08/18/2005 12:04 AM

        To:     biojava-l at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] RNA alignment


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?


Christian Köberle

Max Planck Institut for Infection Biology
Department: Immunology
Schumannstr. 21/22
10117 Berlin

Tel: +49 30 28 460 562
e-mail: koeberle at mpiib-berlin.mpg.de

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