[Biojava-l] Sequence Alignment

[Schreiber, Mark]

> Finally, I think that I will have to come up with a new class 
> encapsulating
> an alignment of multiple very long sequences that overlap on 
> their ends.
> Such as shown below.
> 
> -------------         -----------------
>           ------------------	    --------
>                                      ---------------
> 
> The defined Alignment Interface seems more geared toward alignments of
> multiple homologous sequences.
> 
> ------------xx------
> ---yy----------x----
> z---z-----z---------
> 
> Am I correct in this assumption or am I missing something?
> 
> Thanks,
> 
> David

Hi -

The type of interface for the alignment you want is probably the
AssembledSymbolList


Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand

PH: +64 3 489 9175