[Bioc-sig-seq] gapped alignment

[Kasper Daniel Hansen]

On Apr 24, 2009, at 12:45 , Thomas Girke wrote:

> Thanks for pointing this out. I wasn't aware that such a fast 'SW  
> search'
> option is now available. This will be very useful for many of my own
> applications.

This is simply a consequence of the fact that SW can be pretty fast  
when aligning against a small reference. It won't work in  
'general' (say mammalian genomes).

Kasper