Instructions to run PACMIT in a command line LINUX platform.
-------------------------------------------------------------------------------

This package contains all the files needed to run PACMIT for any set of 3'UTRs
and miRNAs.

'pacmit.pl' and 'rnaplfold.pl' are the two main scripts necessary to obtain the
final list of predictions. Below are examples of how to use them. 

NOTE: If you want to obtain the predictions for PACMIT-0.0 you only need to run
      'pacmit.pl', i.e., you can skip step IV below.

I. REQUIREMENTS:
----------------
The Vienna RNA package version 1.8.X. It can be downloaded at
http://www.tbi.univie.ac.at/RNA.

II. SETTING UP:
---------------
Before running any of the two perl scripts (pacmit.pl and rnaplfold.pl) you need
to edit a couple of lines at the beginning of each file:

1) $BIN_VIENNA should be the path where the Vienna executables are located.
               For example:
               $BIN_VIENNA="/usr/local/bin";
2) $BIN_PACMIT should be the path where all PACMIT executables are contained
               For example:
               $BIN_PACMIT= "/home/$USER/Pacmit_public";

III. INPUT FILES:
-----------------
1) Fasta file with target sequences. Maximum sequence length: 20,000 nucleotides.
2) Fasta file with miRNA sequences. Maximum number of miRNAs: 10,000.

IV. COMPUTING ACCESSIBILITY:
----------------------------
Before running pacmit.pl you will need to fold all the target sequences using
rnaplfold.pl. Type rnaplfold.pl to display the instructions of use.

Example calculations can be run using the sequences provided in Sequences/:

   >cd $BIN_PACMIT/Sequences/Example_utrs/
   >../../rnaplfold.pl example_utr.fa 80 40

You should obtain the following output files:

ENSG00000051596.fa_4
ENSG00000127720.fa_4
ENSG00000161057.fa_4
example_utr.fa
example_utr.vienna

NOTE: By default rnaplfold.pl creates one file per sequence and they are stored
      in the same directory as the fasta file.

V. PREDICTIONS:
---------------
Once accessibilities are computed, you can execute pacmit.pl. Type pacmit.pl
to display the instructions of use.

Example calculations can be run using the sequences provided in Sequences/:

   >cd $BIN_PACMIT
   >./pacmit.pl Sequences/Example_utrs/example_utr.fa Sequences/example_mirna.fa 2 8 1 0.2

The output file should look like this:

#Sequence ID    t_access        No. miRNA       c_access        Expected c_access       log(P_SH)       miRNA name
ENSG00000051596 300     1       2       0.071   -2.625  hsa-miR-186
ENSG00000127720 109     2       1       0.008   -2.080  hsa-miR-212

NOTE: If the 3'UTR fasta file is in the current directory, you have to specify it by
      using the './' notation, otherwise the program will crash. If you type:
      >./pacmit.pl utr_file.fa ...
      the program will crash. You have to type:
      >./pacmit.pl ./utr_file.fa ...

VI. CONTACT US:
---------------
If you have questions, comments or suggestions about the program please
contact us:

jiri.vanicek@epfl.ch
ray.marin@epfl.ch