predictnls (1)

predictnls [\s-1OPTION\s0]

predictnls is a method for the prediction and analysis of nuclear localization signals (\s-1NLS\s0)

Output format

Self-annotating, see example outputs in /usr/share/doc/predictnls/examples.

Cokol, M., Nair, R., and Rost, B. (2000). Finding nuclear localization signals. \s-1EMBO\s0 Rep, 1(5), 411-5.

debug=[0|1]

fileIn=<\s-1FILE\s0>

Input file in fasta format. Required. Only one sequence per file.

fileOut=<\s-1FILE\s0>

Output file. Required.

help

html=[0|1|2]

Output format. 0 - text; 1 - html; 2 - both. Default: 0. If both outputs are requested, the text file is named according to the value of fileOut and the html file gets an `.html' extension.

fileSummary=<\s-1FILE\s0>

If set `1' is written into this file if an \s-1NLS\s0 is found, `0' otherwise. Optional.

nlsdat=<\s-1FILE\s0>

Raw nls data, optional

version

Print version.

\*(C`predictnls fileIn=/usr/share/doc/predictnls/examples/O49931.fa fileOut=/tmp/O49931.nls\*(C'

\s-1PREDICTNLSCONF\s0

Location of predictnlsrc configuration file to use overriding other configuration files

/usr/share/predictnls/predictnlsrc.default

Default configuration file. See this file for a description of the parameters.

/etc/predictnlsrc

System configuration file overriding values in /usr/share/predictnls/predictnlsrc.default

~/.predictnlsrc

User configuration file overriding values in /etc/predictnlsrc If this environment variable is set ~/.predictnlsrc is disregarded and the value of the variable is read for configuration options overriding /etc/predictnlsrc

R. Nair

(C) Copyright 2010, R. Nair License GPLv3+: \s-1GNU\s0 \s-1GPL\s0 version 3 or later <http://gnu.org/licenses/gpl.html>. This is free software: you are free to change and redistribute it. There is \s-1NO\s0 \s-1WARRANTY\s0, to the extent permitted by law.