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Usage
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This software provides a systematic computational framework to detect supercoils of bacterial chromosome. 

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Installation
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Simply put "supercoil.tar.gz" in any directory, 

$ tar zxvf supercoil.tar.gz

enter the folder "supercoil" and type "make" then the compiled codes are within the same directory as the source.

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Inputs and outputs
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The major program in the provided package is `supercoil`, it can parse two 
formats of files, discrete data and continuous data, and examples for each
are provided. See help and look at all available options.

$ ./supercoil -h

1. run the program just consider pathway and microarray information
	
$ ./supercoil -i DATA/NC_000913.expr -j DATA/NC_000913.ptt  -o DATA/NC_000913.gi.operon -p DATA/NC_000913.pathway -n 0.3 -g 0.5 -t 15

2. run the program considering NAP binding sites and HEGs besides pathway and microarray
	
$ ./supercoil -i DATA/NC_000913.expr -j DATA/NC_000913.ptt  -o DATA/NC_000913.gi.operon -p DATA/NC_000913.pathway -a DATA/NC_000913.NAP -e DATA/NC_000913.HEG -D DATA/expression-value -n 0.3 -g 0.5 -t 15

3. identify the weight parameters dynamically [train the parameters (n, g, t) optimizing the accurracy of NAP binding sites mapping]

$ ./supercoil -i DATA/NC_000913.expr -j DATA/NC_000913.ptt  -o DATA/NC_000913.gi.operon -p DATA/NC_000913.pathway -a DATA/NC_000913.NAP -e DATA/NC_000913.HEG -D DATA/expression-value -M

$ perl analysis_dynamic.pl DATA/NC_000913.expr.dynamic > DATA/NC_000913.expr.dynamic.stat

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Changelog
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Version 0.1 
- prototype of algorithm
2011.11.30

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Contact
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Any questions, problems, bugs are welcome and should be dumped to
Qin Ma <maqin2001@gmail.com>

Creation: Dec. 16, 2011

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