PREDICTNLS

NAME

predictnls - prediction and analysis of nuclear localization signals

SYNOPSIS

predictnls [ OPTION ]

DESCRIPTION

predictnls is a method for the prediction and analysis of nuclear localization signals ( NLS )

Output format

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

REFERENCES

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

OPTIONS

debug=[0|1]
fileIn=< FILE >

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

fileOut=< FILE >

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=< FILE >

If set ‘1’ is written into this file if an NLS is found, ‘0’ otherwise. Optional.

nlsdat=< FILE >

Raw nls data, optional

version

Print version.

EXAMPLES

"predictnls fileIn=/usr/share/doc/predictnls/examples/O49931.fa fileOut=/tmp/O49931.nls"

ENVIRONMENT

PREDICTNLSCONF

Location of predictnlsrc configuration file to use overriding other configuration files

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

$PREDICTNLSCONF

If this environment variable is set ˜/.predictnlsrc is disregarded and the value of the variable is read for configuration options overriding /etc/predictnlsrc

AUTHOR

R. Nair

COPYRIGHT AND LICENSE

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