man predictnls (1): 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.