# cobot-tools
Tools for computational biology
# Software required to use cobot-tools
## ViennaRNA
ViennaRNA is a library that already contains lots of useful algorithms that work
with RNA sequences. We use it in order to make tools from cobot-tools better.
Installation guide for Linux can be found [here](https://www.tbi.univie.ac.at/RNA/).
Some issues occur when you try to install ViennaRNA for MacOS. If you want to avoid
them, use the following guide.
### Installation of ViennaRNA for MacOS
Installation of ViennaRNA for MacOS can be done in following steps:
1. Download library. Here is the [link](https://www.tbi.univie.ac.at/RNA/download/sourcecode/2_4_x/ViennaRNA-2.4.13.tar.gz)
for version 2.4.13.
2. Unpack it.
3. Go to the directory, where archive has been unpacked.
4. Run command `./configure --without-perl --without-python`.
5. Remove field `libRNA_la_LDFLAGS` and flag `-static` from the file `src/ViennaRNA/Makefile.am`.
6. Due to us having changed .am-file, it is needed to install following packages: autoconf and automake. In order to do it, run command: `brew install autoconf automake`.
7. Run in the root of library command `autoreconf`.
8. Compile library using command `make -j8` (`j8` - flag that allows us to compile code using 8 jobs).
9. Run command `make install`.
# Tools of cobot-tools
## Sequence.Primer.Optimisation.designPrimer
Given 'DNA' sequence and position in that sequence designs forward primer for that sequence.
Primer will start at the given position.