csb-buildhmm1

Build an hmm from a fasta sequence

Overview

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)

Releases

Unchanged in 4 releases since Debian 10 (Buster).

10–13