CodonO web service readme file for home_directory/downloads/

The "CU" program version 2.0 compute the Synonymous Codon Usage Order (SCUO) 
for the input sequences. The SCUO measures the codon usage bias and 
it is fit for codon usage comparison within and across genome.

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   It was written by Xiufeng (Henry) Wan, Environmental Sciences Division, Oak Ridge
   National Laboratory, Oak Ridge, TN 37831 and updated by Mike Angellotti from
	Systems Biology Laboratory, Department of Microbiology at Miami University.
  
   This program is free software. This program is distributed in the hope that
   it will be useful, but  WITHOUT ANY WARRANTY; without even the implied 
   warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

   Any bug should refer to Dr. Henry Wan by e-mail: wan@cvm.msstate.edu or wanhenry@yahoo.com.

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This directory should contain the following files: CU.aix, CU.linux, CU.Win2000.exe

CU.aix for IBM AIX platform 
CU.linux for Linux platform
CU.Win2000.exe for Windows 32 platform

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Running command:
	./command inputfile

	Input file format should be in Fasta format. The example of fasta sequence
	can be found at http://en.wikipedia.org/wiki/Fasta_format.
	
	    Four output files:
		      inputfile.ok  ---- the SCUO units for each input sequences based on their order 
		      inputfile.fik ---- the composition ratio of the i-th amino acid in the k-th sequence
		      inputfile.hijk---- the frequency of the j-th degenerate codon for amino acid i in each sequence
		      inputfile.iik ---- the degree of orderliness for synonymous codon usage for the i-th amino acid in each sequence
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Documents for citing:
1. Wan, X.-F., J. Zhou, and D. Xu. 2006. CodonO: a new informatics method
measuring synonymous codon usage bias. International Journal of General
Systems, 35: 109-125.

2. Wan, X.-F., D. Xu, A. Kleinhofs, and J. Zhou. 2004. Quantitative
relationship between codon usage bias and GC composition across the
unicellular genomes. BMC Evolutionary Biology, 4: 19
http://www.biomedcentral.com/1471-2148/4/19/

3. Wan, X., D. Xu, and J. Zhou. 2003. A new informatics method measuring
synonymous codon usage bias. In Intelligent engineering systems through
artificial neural networks, vol 13, eds. Dagli et al., 1101-1018. New York,
NY: ASME Press.
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