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

[Thomas Down]

On Mon, Jan 22, 2001 at 02:24:44PM +1300, Mark Schreiber wrote:
> Hi,
> 
> I am fairly familiar with HMM's but I am not shure what is meant by the
> term double headed. Can someone explain??

Not absolutely sure where the terminology originates but it
refers to the number of sequences emitted by the model:

  - Single-head models emit a single sequence.  The dp toolkit
    can be used to align and score a sequence against the model.
    Profile HMMs for recognising protein families would be a
    classic application.  In biojava, these models generally
    emit over simple alphabets (eg DNA or protein).

  - Two-head models emit a pair of sequences.  They can be used
    to align and score two sequences against one another.  Alignment
    algorithms such as Smith-Waterman can be implemented as
    a two-head HMM.  They always emit over cross-product alphabets
    (e.g. DNA x DNA).

One day, it would be nice to upgrade the toolkit so that it
can dynamically generate arbitrary-headed DP algorithms (i.e.
for alighning three or more sequences).

Hope this clarifies matters,

    Thomas.