conkit.applications.hhblits module¶
Command line object for HHblits Multiple Sequence Alignment application
-
class
HHblitsCommandline
(cmd='hhblits', **kwargs)[source]¶ Bases:
Bio.Application.AbstractCommandline
Command line object for HHblits [1] [2] alignment generation
https://toolkit.tuebingen.mpg.de/hhblits
The HHblits program is a homology detection tool by iterative HMM-HMM comparison.
[1] Alva V., Nam SZ., Söding J., Lupas AN. (2016). The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res. pii: gkw348. [2] Remmert M., Biegert A., Hauser A., Söding J. (2011). HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods. 9(2):173-5. Examples
To generate a Multiple Sequence Alignment, use:
>>> from conkit.applications import HHblitsCommandline >>> hhblits_cline = HHblitsCommandline( ... input="test.fasta", database="uniprot20_29Feb2012" ... ) >>> print(hhblits_cline) hhblits -i test.fasta -d uniprot20_29Feb2012
You would typically run the command line with
hhblits_cline()
or via thesubprocess
module.