Install Target Finder on Mac

TargetFinder predicts microRNA targets with a plant-specific scheme. To install it on Mac:

1. Download the current release of TargetFinder, now it is Release 1.6

2. Extract and read the README and INSTALL files

3. Download fasta as requested at http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml

   Current version is fasta36.

4. Extract and read the README file

5. To install the standard FASTA programs:

cd src
make -f ../make/Makefile.linux_sse2 all

The executable programs will appear in ../bin

1. Make a copy of the executable fasta36 program in your PATH

   To check your system PATH:

echo $PATH

Copy fasta36 to /usr/bin (for example) and rename it to fasta35 (a quick-and-dirty way to make TargetFinder work. A better way is to change line 88 of targetfinder.pl to my $fasta = “fasta36”;):

sudo cp ../bin/fasta36 /usr/bin/fasta35

1. Run TargetFinder: Dir_to_targetfinder/targetfinder.pl -s miRNA.fa -d targets.fa