API Reference

Cython bindings and Python interface to HMMER3.

HMMER is a biological sequence analysis tool that uses profile hidden Markov models to search for sequence homologs. HMMER3 is maintained by members of the the Eddy/Rivas Laboratory at Harvard University.

pyhmmer is a module, implemented using the Cython language, that provides bindings to HMMER3. It directly interacts with the HMMER internals, which has several advantages over CLI wrappers like hmmer-py.

HMMER

pyhmmer.hmmer.hmmsearch

Search HMM profiles against a sequence database.

pyhmmer.hmmer.phmmer

Search protein sequences against a sequence database.

pyhmmer.hmmer.hmmpress

Press several HMMs into a database.

Easel

pyhmmer.easel.Alphabet

A biological alphabet, including additional marker symbols.

pyhmmer.easel.Bitfield

A statically sized sequence of booleans stored as a packed bitfield.

pyhmmer.easel.DigitalMSA

A multiple sequence alignment stored in digital mode.

pyhmmer.easel.DigitalSequence

A biological sequence stored in digital mode.

pyhmmer.easel.KeyHash

A dynamically resized container to store string keys using a hash table.

pyhmmer.easel.MSA

An abstract alignment of multiple sequences.

pyhmmer.easel.Sequence

An abstract biological sequence with some associated metadata.

pyhmmer.easel.SequenceFile

A wrapper around a sequence file, containing unaligned sequences.

pyhmmer.easel.TextMSA

A multiple sequence alignement stored in text mode.

pyhmmer.easel.TextSequence

A biological sequence stored in text mode.

pyhmmer.easel.SSIReader

A read-only handler for sequence/subsequence index file.

pyhmmer.easel.SSIWriter

A writer for sequence/subsequence index files.

Plan7

pyhmmer.plan7.Alignment

A single alignment of a sequence to a profile.

pyhmmer.plan7.Background

The null background model of HMMER.

pyhmmer.plan7.Domain

A single domain in a query Hit.

pyhmmer.plan7.Domains

A sequence of domains corresponding to a single Hit.

pyhmmer.plan7.Hit

A high-scoring database hit found by the comparison pipeline.

pyhmmer.plan7.HMM

A data structure storing the Plan7 Hidden Markov Model.

pyhmmer.plan7.HMMFile

A wrapper around a file (or database), storing serialized HMMs.

pyhmmer.plan7.OptimizedProfile

An optimized profile that uses platform-specific instructions.

pyhmmer.plan7.Pipeline

An HMMER3 accelerated sequence/profile comparison pipeline.

pyhmmer.plan7.Profile

A Plan7 search profile.

pyhmmer.plan7.TopHits

A ranked list of top-scoring hits.

Errors

pyhmmer.errors.AllocationError

A memory error that is caused by an unsuccessful allocation.

pyhmmer.errors.UnexpectedError

An unexpected error that happened in the C code.

pyhmmer.errors.EaselError

An error that was raised from the Easel code.