HMMER (pyhmmer.hmmer)

Reimplementation of HMMER binaries with the PyHMMER API.

Note

Functions of this module handle parallelization using threads to run searches in parallel for the different queries. If less queries are given, the number of threads will be reduced to avoid spawning idle threads.

Sequence Searches

hmmsearch(queries, sequences, *[, cpus, ...])	Search HMM profiles against a sequence database.
hmmscan(queries, profiles, *[, cpus, ...])	Scan query sequences against a profile database.

Profile Searches

phmmer(queries, sequences, *[, cpus, ...])	Search protein sequences against a sequence database.
nhmmer(queries, sequences, *[, cpus, ...])	Search nucleotide sequences against a sequence database.

Iterative Searches

jackhmmer(queries, sequences, *[, ...])

Search protein sequences against a sequence database.

Utilities

hmmpress(hmms, output)	Press several HMMs into a database.
hmmalign(hmm, sequences, *[, digitize, ...])	Align several sequences to a reference HMM, and return the MSA.