[Seqan-dev] SwiftLocal specialization with Hamming distance

[Fabian Buske <f.buske@uq.edu.au>]

Hi,

I'm currently converting my project from SeqAn release 1.2 to the svn 
trunk. Doing this I realized that there has been quite a few changes 
going on.

I have a couple of questions that I hope you can comment on.

Is there a reason that there is no Hamming-specialization of the 
SwiftLocal  swift-algorithm (find_swift)? Since I'm keen on using a 
local alignment filter with Hamming distance I would be grateful if that 
could be added.

Secondly, in the same algorithm ndlPos seems to be particular 
interesting for the Hamming distance version, since it could potentially 
speed up any verification due to the known offset of the needle and the 
haystack to each other. Which from the set of available algorithms would 
be most suited for the validation, i.e. does approximate matching 
without indels returning all alignments that fulfill a minimum size and 
error rate criteria.

Cheers,
Fabian

--
Fabian Buske
Institute for Molecular Bioscience
The University of Queensland 
Brisbane, Qld. 4072 Australia
Phone: (61)-(7)-334-62608