[Dynamite] (no subject)

[Ian Holmes]

On Mon, 24 Jul 2000, Guy Slater wrote:

> > > > As soon as we have genewise we will want linear space algorithms ;)
> > > 
> > > I was assuming we were going to do something like:
> > > 
> > >     find_score_only() --> find_end_points() --> global_traceback()
> > 
> > 
> > This is indeed the case of how I imagine it. Actually - miss out score
> > only part - go straight to find_end_points. 
> 
> score_only is just for the database search part.
>  
> > with special states (not sure what the telegraph equivalent is) an
> > important optimisation is to find the set of special state start/end
> > points in one sweep followed by "local" global alignments.
> 
> I'm not sure about how special states will be handled either,
> but I think Ian and I discussed this at some point.  Ian ? 

I had in mind something like:

  <state name="my_special_state/">
    <loop chain="target"/>    <!--this is the tag that indicates it's a special state-->
    ...
  </state>

...i.e. s/special/loop/

but otherwise they're handled the same as dynamite