Bioinformatics 1

This is a project from the 'Bioinformatics 1' course at the Faculty of Electrical Engineering and Computing (FER).

Course information can be found here.

Goal of this project is to implement the high-speed and high-ratio referential genome compression algorithm. Original article can be found here and the original repository can be found here.

Comparison of our results and the original implementation can be found in the documentation file.

Example on how to run the program can be found below.

Authors

• Katarina Mišura
• Marko Marfat

Necessary prerequisites

• MinGW
• 7zip

NOTE: This code is meant to be run on a Linux operating system.

Compile

g++ hirgc.cpp -o hirgc -O3
g++ de_hirgc.cpp -o de_hirgc -O3

Run

./hirgc -r reference.fa -t target.fa
./de_hirgc -r reference.fa -t output.7z

NOTE: Use the provided test2ref.fa as reference and test2tar.fa as target.

./hirgc is used for compression
./de_hirgc is used for decompression