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.