table of contents
| CSB-BUILDHMM(1) | User Commands | CSB-BUILDHMM(1) |
NAME¶
csb-buildhmm - build an HMM from a FASTA sequence
DESCRIPTION¶
usage: csb-buildhmm [-h] -q QUERY_ID [-t TK_ROOT] [-d DATABASE] [-c TK_CONFIG]
- [--cpu CPU] [--no-ss] [--no-pseudo] [--no-calibration]
- query
Build an HMM from a FASTA sequence. This program is a proxy to hhblits/addss.pl and hhmake from the HHpred package. @note: assuming you have the full HHpred package installed and configured.
positional arguments:¶
- query
- input sequence (FASTA or PDB file)
optional arguments:¶
- -h, --help
- show this help message and exit
- -q QUERY_ID, --query-id QUERY_ID
- ID of the query, in PDB-like format (accessionCHAIN).Used for naming the output files. Also, if the input is a PDB file with multiple chains, CHAIN is used to pull the required chain from the file.
- -t TK_ROOT, --tk-root TK_ROOT
- path to the ToolkitRoot folder in your HHsuite setup (default=/ebio/abt1_toolkit/share/wye)
- -d DATABASE, --database DATABASE
- custom HHblits database; if not defined, toolkit's unirpto20 will be used
- -c TK_CONFIG, --tk-config TK_CONFIG
- path to a folder containing custom HHsuite configs (e.g. HHPaths.pm) (default=.)
- --cpu CPU
- maximum degree of parallelism (default=1)
- --no-ss
- do not include secondary structure (default=False)
- --no-pseudo
- do not add emission and transition pseudocounts (default=False)
- --no-calibration
- do not calibrate the profile (default=False)
AUTHOR¶
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
| November 2017 | csb-buildhmm 1.2.5 |