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¶
Search HMM profiles against a sequence database. |
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Search protein sequences against a sequence database. |
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Search nucleotide sequences against a sequence database. |
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Press several HMMs into a database. |
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Align several sequences to a reference HMM, and return the MSA. |
Easel¶
Data Structures¶
A statically sized sequence of booleans stored as a packed bitfield. |
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A dynamically resized container to store byte keys using a hash table. |
Sequences¶
An abstract biological sequence with some associated metadata. |
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A biological sequence stored in text mode. |
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A biological sequence stored in digital mode. |
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A wrapper around a sequence file, containing unaligned sequences. |
Alignments¶
An abstract alignment of multiple sequences. |
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A multiple sequence alignement stored in text mode. |
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A multiple sequence alignment stored in digital mode. |
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A wrapper around a multiple-alignment file. |
Linear Algebra¶
An abstract 1D array of fixed size. |
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A vector storing single-precision floating point numbers. |
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A vector storing byte-sized unsigned integers. |
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An abstract 2D array of fixed size. |
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A matrix storing single-precision floating point numbers. |
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A matrix storing byte-sized unsigned integers. |
Miscellaneous¶
A biological alphabet, including additional marker symbols. |
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A portable, thread-safe random number generator. |
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A read-only handler for sequence/subsequence index file. |
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A writer for sequence/subsequence index files. |
Plan7¶
Profile¶
A Plan7 search profile. |
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An optimized profile that uses platform-specific instructions. |
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The null background model of HMMER. |
Pipelines¶
An HMMER3 accelerated sequence/profile comparison pipeline. |
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An HMMER3 pipeline tuned for long targets. |
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A factory for constructing new HMMs from raw sequences. |
Results¶
A ranked list of top-scoring hits. |
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A high-scoring database hit found by the comparison pipeline. |
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A read-only view over the domains of a single |
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A single domain in a query |
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An alignment of a sequence to a profile. |
Traces¶
A factory for aligning several sequences to a reference model. |
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A list of tracebacks obtained by aligning several sequences to a model. |
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A traceback for the alignment of a model to a sequence. |
Miscellaneous¶
A mutable view over the score cutoffs of a |
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A mutable view over the e-value parameters of a |
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A mutable view over the disk offsets of a profile. |
Errors¶
A memory error that is caused by an unsuccessful allocation. |
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An unexpected error that happened in the C code. |
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An error that was raised from the Easel code. |