Plan7 (pyhmmer.plan7)

High-level interface to the Plan7 data model.

Plan7 is the model architecture used by HMMER since HMMER2.

See also

Details about the Plan 7 architecture in the HMMER documentation.

Profile Hidden Markov Models

HMM	A data structure storing the Plan7 Hidden Markov Model.
Profile	A Plan7 search profile.
OptimizedProfile	An optimized profile that uses platform-specific instructions.
OptimizedProfileBlock	A container for storing OptimizedProfile objects.

Parsers

HMMFile	A wrapper around a file (or database), storing serialized HMMs.
HMMPressedFile	An iterator over each OptimizedProfile in a pressed HMM database.

Pipelines

Pipeline	An HMMER3 accelerated sequence/profile comparison pipeline.
LongTargetsPipeline	An HMMER3 pipeline tuned for long targets.
Builder	A factory for constructing new HMMs from raw sequences.
Background	The null background model of HMMER.

Results

TopHits	An immutable ranked list of top-scoring hits.
Hit	A high-scoring database hit found by the comparison pipeline.
Domains	A read-only view over the domains of a single Hit.
Domain	A single domain in a query Hit.
Alignment	An alignment of a sequence to a profile.

Traces

TraceAligner	A factory for aligning several sequences to a reference model.
Traces	A list of tracebacks obtained by aligning several sequences to a model.
Trace	A traceback for the alignment of a model to a sequence.

Iterative Searches

IterativeSearch	A helper class for running iterative queries like JackHMMER.
IterationResult	The results of a single iteration from an IterativeSearch.

Miscellaneous

Cutoffs	A mutable view over the score cutoffs of a HMM or a Profile.
EvalueParameters	A mutable view over the e-value parameters of a HMM or a Profile.
Offsets	A mutable view over the disk offsets of a profile.
Transitions(value[, names, module, ...])	A helper enum for indices of the HMM transition probability matrix.