Command line object for Jackhmmer Multiple Sequence Alignment generation
JackhmmerCommandline
(cmd=’jackhmmer’, **kwargs)[source]¶Bases: Bio.Application.AbstractCommandline
Command line object for Jackhmmer [1] alignment generation
Jackhmmer is an algorithm that uses iterative searches a protein sequence against a protein sequence database to find sequence homologs.
[1] | Johnson L. S., Eddy S. R., Portugaly E. (2010). Hidden Markov Model Speed Heuristic and Iterative HMM Search Procedure. BMC Bioinformatics 11, 431. |
Examples
To generate a Multiple Sequence Alignment, use:
>>> from conkit.applications import JackhmmerCommandline
>>> jackhmmer_cline = JackhmmerCommandline(
... input="test.fasta", database="uniref100.fasta"
... )
>>> print(jackhmmer_cline)
jackhmmer test.fasta uniref100.fasta
You would typically run the command line with jackhmmer_cline()
or via
the subprocess
module.