mkseed is a simple tool that aims to find microRNA seed sites.
mkseed has been developed with C++ and SeqAn. mkseed uses several algorithms provided by SeqAn to find microRNA target sites.
- Suffix array
- N-mer
- Horspool's algorithm
- Brute-force
mkseed 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 mkseed only provides a single executable.
| Program | Description |
|---|---|
| find_seed | Find microRNA seed sites in mRNA sequences |
find_seed requires three command line arguments to process seed finding.
| Input | Description |
|---|---|
| miRNA fasta file name | micorRNA sequences in Fasta format |
| mRNA fasta file name | messengerRNA sequences in Fasta foramt |
| Output file name | Output results will be written in this file |
find_seed /path/to/mirna.fasta /path/to/mrna.fasta /path/to/output.txt