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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Press several HMMs into a database. |
Easel¶
A biological alphabet, including additional marker symbols. |
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A statically sized sequence of booleans stored as a packed bitfield. |
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A multiple sequence alignment stored in digital mode. |
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A biological sequence stored in digital mode. |
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A dynamically resized container to store string keys using a hash table. |
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An abstract alignment of multiple sequences. |
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An abstract biological sequence with some associated metadata. |
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A wrapper around a sequence file, containing unaligned sequences. |
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A multiple sequence alignement stored in text mode. |
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A biological sequence stored in text mode. |
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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¶
A single alignment of a sequence to a profile. |
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The null background model of HMMER. |
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A single domain in a query |
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A sequence of domains corresponding to a single |
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A high-scoring database hit found by the comparison pipeline. |
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A data structure storing the Plan7 Hidden Markov Model. |
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A wrapper around a file (or database), storing serialized HMMs. |
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An optimized profile that uses platform-specific instructions. |
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An HMMER3 accelerated sequence/profile comparison pipeline. |
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A Plan7 search profile. |
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A ranked list of top-scoring hits. |
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. |