Package hmm

source code

HHpred and Hidden Markov Model APIs.

This package defines the abstractions for working with HHpred's HMMs and hit lists. ProfileHMM is the most important object of this module. It describes a sequence profile hidden Markov model in the way HHpred sees this concept:

• a profile is composed of a list of HMMLayers, which contain a number of States
• these States can be of different types: Match, Insertion Deletion, etc.
• a profile contains a multiple alignment, from which it is derived
• this multiple alignment is an A3M (condensed) Alignment, where the first sequence is a master sequence
• the match states in all layers correspond to the residues of the master sequence

ProfileHMM objects provide list-like access to their layers:

>>> hmm.layers[1]
<HMMLayer>    # first layer: layer at master residue=1

Every layer provides dictionary-like access to its states:

>>> layer[States.Match]
<Match State>

and every state provides dictionary-like access to its transitions to other states:

>>> state = hmm.layers[1][States.match]
>>> state.transitions[States.Insertion]
<Transition>       # Match > Insertion
>>> transition.predecessor
<Match State>      # source state
>>> transition.successor
<Insertion State>  # target state

Whether this transition points to a state at the same (i) or the next layer (i+1) depends on the semantics of the source and the target states.

Building HMMs from scratch is supported through a number of append methods at various places:

>>> layer = HMMLayer(...)
>>> layer.append(State(...))
>>> hmm.layers.append(layer)

See HMMLayersCollection, HMMLayer, EmissionTable and TransitionTable for details.