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===================== TEST SUITE FOR RIsearch2 ==========================
=========================================================================

 This is a test directory for RISearch2 containing some query and target
 sequences to be able to test-run it on a very small dataset.

 !!! query.fa and target.fa files are the actual files used to generate
 !!! the examples given in the User Manual

 Our test case is predicting the binding sites of hsa-miR-24-3p and
 hsa-miR-876-5p miRNAs on the transcripts that are part of Rhoc gene
 (ENSG00000155366). Note that this gene has already been reported as
 target gene for these miRNAs.

 1) In order to carry out the predictions, you first need to build the 
    index structure of target sequence by using the RIsearch2 itself. 
    You can do this by executing the following commands. 
    (Replace the "path_to_the_code_package" with correspondig path.)

    cd /path_to_the_code_package/test_suite/
    ../bin/risearch2.x -c RHOC.fa -o RHOC.pksuf
 
 2) After this, you can continue to prediction stage and run RIsearch2
    with default parameter settings (-s6 -l 20 -e -20) by typing:

    ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf
 
 3) Executing the above command should have generated two files in this
    directory that contains the binding sites predicted on these transcripts
    and their antisense. Predictions on antisense are labeled with "-" in 
    these files. Filenames are 
    "risearch_hsa-miR-24-3p.out.gz" and "risearch_hsa-miR-876-5p.out.gz"
    You can see all predictions with the following command.

    zcat risearch_hsa-miR-24-3p.out.gz risearch_hsa-miR-876-5p.out.gz

    ... or to see the results excluding the binding sites on antisense.

    zcat risearch_hsa-miR-* | grep '+'

 4) You can also compare the results you obtained for hsa-miR-24-3p
    with our precompiled results to make sure that RIsearch2 is working. 
    Type the next command and if you dont see any warning,
    it means everything is working well.
    
    diff risearch_hsa-miR-24-3p.out.gz precompiled_results

 5) As you might have noticed, there are no binding sites predicted on
    hsa-miR-876-5p transcript. This is due to low default energy 
    threshold (-20) for miRNA interactions. You can change this threshold 
    in following way. (PLEASE READ THE USER MANUAL as well!)

    ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf -e -15
    zcat risearch_hsa-miR-* | grep '+'

    Now you can see that there are two binding sites predicted for that
    miRNA as well.
 
 6) Now lets try with conventional miRNA seed constraints.
    (PLEASE READ THE USER MANUAL!)

   ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf -e -15 -s 2:7
   zcat risearch_hsa-miR-* | grep '+'

 7) Play around by changing the seed, energy and the other parameter settings.
    Note that with each run you will overwrite the results from previous
    run as long as you keep working in this directory. A few example runs;

    ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf -e -15 -s 2:7/5
    ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf -e -10 -s 2:7
    ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf -e -15 -s 6 -l 0
    ../bin/risearch2.x -q mirnas.fa -i RHOC.pksuf -e -15 -s 2:7/5 -p2

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    Please read the USER MANUAL to understand all parameters you can
    set when running RIsearch2 and you are very much encouraged to try
    making new RIsearch2 predictions with different constraint settings.

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