[Biojava-l] Is there a Java implementation of SW that also returns N suboptimal alignments

[Matthew Pocock]

Hi David,

There may be people on the list with dedicated sw
code. I always use the BioJava dynamic programming
library for this sort of thing. However, currently it
only returns the optimal alignment. Sub-optimal
alignments are definitely on my to-do list, but won't
happen within the next month.

Matthew

 --- David Nix <nix at uclink.berkeley.edu> wrote: 
> Hello Folks,
>     I'm looking for a local alignment script that
> uses a variant of the
> Smith-Waterman algorithm where, in addition to the
> highest scoring
> alignment, all other alignments above a given score
> cut off are returned.
> Two such programs have already been written in C
> (LALIGN and SIM), but I
> would like to use all native code in my application
> to preserve the Java
> portability.  Any suggestions? -cheers, Dave
> 
> 
> -- 
> David Austin Nix, PhD
> University of California at Berkeley
> Lawrence Berkeley National Lab
> Mailstop 84-171
> One Cyclotron Road
> Berkeley, CA  94720-3200
> 
> 510-486-6791 (lab)
> 510-786-549-0137 (fax)
> Nix at uclink.berkeley.edu
> 
> 
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