[Dynamite] (no subject)

[Ewan Birney]

On Tue, 25 Jul 2000, Ian Holmes wrote:

> On Wed, 26 Jul 2000, Ewan Birney wrote:
> 
> > 
> > > ...this is not total fluff---the point is that loop states change the
> > > actual functionality of the model, whereas singlet states that aren't loop
> > > states (like INSERT_QUERY_* above) don't change the functionality (the
> > > scores returned by algorithms will be the same; it will just shave a bit
> > > off the running time of the algorithm because you don't store a whole
> > > bunch of empty cells in the matrix).
> > 
> > 
> > No. Because there are singlet->singlet potential transitions and the
> > viterbi or posterior score when we jump into the polymer matrix is data
> > dependent and path (through singlet) dependent.
> > 
> 
> Would you mind illustrating this with an example please? I am not
> convinced that singlet states can't be auto-detected and I think I may not
> be understanding your point.


In genewise the pre-matrix special states are

   PRE_CODON, PRE_INTRON_1, PRE_INTRON2, PRE_INTRON3 

ie, a full mini-genscan parser.


This means you can't factor out these states; you do have to calculate
them.

perhaps I am missing your point. hmmmmmmmmm.



> 
> Either way, I have now come round to the idea that we should label all
> special states, pretty much exactly the way Dynamite does, except that we
> should call them "singlet" not "special". And yes, on reflection "singlet"
> is a much better name than "loop".
> 
> So, just to be clear, a special state looks like this:
> 
> 	<state name="fred"> <singlet chain="target"/> </state>
> 
> whereas a regular state looks like this
> 
> 	<state name="jim"> </state>
> 
> or, equivalently
> 
> 	<state name="jim"/>
> 
> For now, I think we should also (being nice to Guy) stipulate that the
> state order that passes through the XML layer (from me to Guy) can be used
> unchanged, i.e. I will pre-sort the states so that singlets and null
> transitions are handled nicely.
> 
> Ian
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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