[Dynamite] (no subject)

[Ewan Birney]

On Mon, 24 Jul 2000, Ian Holmes wrote:

> 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
> 

Hmmm. Neither "loop" nor "special" really capture their attributes 
(states can be special without looping. true? it is so in dynamite)


How about "singlet" states (ie, not polymer). or "monomer"