[Biojava-l] single and double headed HMM's

[Mark Schreiber]

On Mon, 22 Jan 2001, Matthew Pocock wrote:

> Hi.
> 
> Mark Schreiber wrote:
> 
> A traditional one-head model would be a trans-membrain model, a profile HMM
> or a MEME weight-matrix. A traditional example of a two-head model would be
> pair-wise alignment, or aligning protein to genomic sequences. MSA performs
> n-head alignment to give you the (nearly) optimal alignment of n sequences.
> Each head may have a distinct alphabet - you could align DNA and PROTEIN
> and cDNA if you wanted - if you could think of something usefull that this
> did. An obvious and fun 3 head algorithm would be to align genomic to
> genomic via cDNA or PROTEIN to make a comparative gene finder.
> 
> Should this go into the docs somewhere?

Sure, how about in the package for one headed and two headed?

Mark


> 
> >
> >
> > Mark
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Mark Schreiber                  Ph: 64 3 4797875
> > Rm 218                          email mark_s@sanger.otago.ac.nz
> > Department of Biochemistry      email m.schreiber@clear.net.nz
> > University of Otago
> > PO Box 56
> > Dunedin
> > New Zealand
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
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> 
> 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Mark Schreiber			Ph: 64 3 4797875
Rm 218				email mark_s@sanger.otago.ac.nz
Department of Biochemistry	email m.schreiber@clear.net.nz
University of Otago		
PO Box 56
Dunedin
New Zealand
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~