conkit.applications.jackhmmer module¶
Command line object for Jackhmmer Multiple Sequence Alignment generation
-
class
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 thesubprocess
module.