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DESCRIPTION: Tool for the identification and localization of
	(I)  all canonical Hypoxia-Response Elements (HRE) 
	(II) all functional HRE (localization of Hypoxia-Anciliary Sequences (HAS) towards downstream from HRE on spaces of 7-15 nt)

PROGRAM EXECUTION:

	#perl HREFinder.pl <FASTA file>
	<FASTAfile>    Single file in FASTA format containing the sequence(s).
	EXAMPLE: #perl misa.pl PATH/sequence.fasta or #perl misa.pl PATH/sequence.txt
OUTPUT
	This program generates three output files  in the working directory with the prefix of the file name of the input sequence
	'sequence_AllMinedHRE.txt' contains all identified HRE in both strands
	'sequence_FunctionalHRE.txt' contains all predicted functional HRE in both strands
	'sequence_HREFrequencyTable.txt' contains all frequencies of HRE distribution in every 500 nt consecutive fragment set of supplied sequences
Test
	The 'TestDataSet' directory  contains input sequence files which were used in test studies
	The 'ResultsTestDataSet'  directory contains output files of all example input sequences


**The user provided query sequences in the HREFinder are being considered the forward strand sequences