predictnls1

Usage

Overview

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

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

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.