Information:
---------------------------------------------------------------
This directory contains a set of various computer code used in
	 Gilchrist, Qin, and Zaretzki (2007) BMC-Bioinformatics
please kindly cite this paper when using any of this code
 
All code is released under GPL v2 and without any warranty, stated
or implied.  The author for each set of code may be contacted for
help.

All code has a README file describing what it does and how to execute
it.

A brief description is as follows
	identify.tag.sites -- written in PERL, used to parse FASA
		file to identify potential SAGE tag sites

	est.cutting.efficiency -- written in R, used to generate
		a table of log likelihood values for the cutting
		efficiency of the anchoring enzyme used in a SAGE
		tag experiment
	calc.marg.post -- written in Mathematica.  Used to generate
		posterior pdfs and such for the mRNA abundance of each
		individual gene
	sim.joint.post -- Written in R. Uses an MCMC method to
		simulate mRNA population. Output can be used to infer
		information on the joint and marginal distributions 
		of the mRNA abundances for individual genes