psort - bacterial localization prediction tool
psort [-p|-n] [OPTIONS] [SEQFILE]
Runs psort on the sequence file SEQFILE . If SEQFILE isn't
provided then sequences will be read from STDIN.
- --help,
-h
- Displays usage information
- --positive,
-p
- Gram positive bacteria
- --negative,
-n
- Gram negative bacteria
- --archaea,
-a
- Archaea
- --cutoff,
-c
- Sets a cutoff value for reported results
- --divergent,
-d
- Sets a cutoff value for the multiple localization flag
- --matrix,
-m
- Specifies the path to the pftools installation. If not set, defaults to
the value of the PSORT_PFTOOLS environment variable.
- --format,
-f
- Specifies sequence format (default is FASTA)
- --exact,
-e
- Skip SCLBLASTe (useful for batch runs of data against itself in
SCLBLAST)
- --output,
-o
- Specifies the format for the output (default is 'normal' Value can be one
of: terse, long or normal
- --root,
-r
- Specify PSORT_ROOT for running local copies. If not set, defaults to the
value of the PSORT_ROOT environment variable.
- --server,
-s
- Specifies the PSort server to use
- --verbose,
-v
- Be verbose while running
--x-skip-localization
- --version
- Print the version of PSortb
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.