mikan provides an ensemble approach to combine six different miRNA target prediction algorithms.
- TargetScan
- PITA
- RNAhybrid
- miRanda
- TargetMiner
- Two-step SVM
mikan bundles all dependent header libraries and uses CMake to compile the source code.
Example on Linux/Unix/OS X
mkdir build
cd build
cmake -D CMAKE_INSTALL_PREFIX=/path/to/install -D CMAKE_BUILD_TYPE=Release ../src
make && make install
The current version of mikan provides an ensemble program as well as individual programs for each algorithm. .
| Program | Description |
|---|---|
| mikan | mikan ensemble algorithm |
| mkconf | Show default configuration values to stdout |
| mk-targetscan | mikan version of TargetScan implementation |
| mk-pita | mikan version of PITA implementation |
| mk-rhahybrid | mikan version of RNAhybrid implementation |
| mk-miranda | mikan version of miRanda implementation |
| mk-targetminer | mikan version of TargetMiner implementation |
| mk-twostep-svm | mikan version of Two-step SVM implementation |
mikan and all mk-* programs require four command line arguments.
| Input | Description |
|---|---|
| miRNA fasta file name | micorRNA sequences in Fasta format |
| mRNA fasta file name | mRNA sequences in Fasta foramt |
| Output file name 1 | Site level scores are written in this file |
| Output file name 2 | RNA level scores are written in this file |
mikan /path/to/mirna.fasta /path/to/mrna.fasta /path/to/output1.txt /path/to/output2.txt