NAME¶

psort - bacterial localization prediction tool

SYNOPSIS¶

psort [-p|-n] [OPTIONS] [SEQFILE]

DESCRIPTION¶

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

AUTHOR¶

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.