INTRODUCTION
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The JAVA program TargetSpy predicts microRNA target sites without requiring a perfect seed match nor cross-species information.
For prediction two input files are required:
	1) a fasta file with the microRNA sequences
	2) a fasta file with the sequences of the 3'UTRs

Input files can also be provided in a gzipped version.


INSTALLATION AND CONFIGURATION
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To install TargetSpy,
1) Extract the TargetSpy package and copy the TargetSpy directory to your preferred location
2) Alter the "InstPath" in TargetSpy/bin/TargetSpy with respect to your location
3) Install the Vienna RNA Package, Version 1.6.1. Copy the executable of RNAduplex to the TargetSpy/share directory.

Note: Only use exactly version 1.6.1 of the Vienna RNA Package.

EXECUTION
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Type "TargetSpy -h" to get an overview of the commandline parameters.


EXAMPLE
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To run the sample data change to the 'sample' directory and type the following command:

	../bin/TargetSpy -microRNAs miRNA_demo.gz -transcripts transcripts_demo.gz

If you have added TargetSpy to your PATH variable you can also execute the following command:
	
	TargetSpy -microRNAs miRNA_demo.gz -transcripts transcripts_demo.gz

A result.gz file will be written to the sample directory.

You can find pre-calculated sample data in the result_demo.gz file.