• This is the official github repository of NASCUP: Nucleic Acid Sequence Classification by Universal Probability.
• This repository is still under construction.

You can install NASCUP by cloning our git repository and making executable files from the source codes:

git clone https://github.com/nascup/nascup.git
cd nascup
g++ -O2 -Wall -fopenmp -o nascupbuild train.cpp
g++ -O2 -Wall -fopenmp -o nascupscan test.cpp

You can train context tree models of each group by running nascupbuild. For example, ./nascupbuild -i train.fasta -o model.ctm creates model.ctm from train.fasta.

You can classify query sequences based on context tree models by running nascupscan. For example, after running ./nascupscan -c model.ctm -i test.fasta -o result.out, result.out includes labels of given queries in test.fasta.

For the datasets we used in the paper can be downloaded as follows:

wget https://data.snu.ac.kr/nascup/data/[FILENAME].tar.gz

[FILENAME] are b_RF, b_RD, b_GG, b_SS, b_SL, b_AR, b_DV, 10BGG for RF, RD, GG, SS, SL, AR, DV, BGG dataset, respectively.

If you use NASCUP in your research, please cite our paper:

@article{kwon2015nascup,
title={NASCUP: Nucleic Acid Sequence Classification by Universal Probability},
author={Kwon, Sunyoung and Kim, Gyuwan and Lee, Byunghan and Yoon, Sungroh and Kim, Young-Han},
journal={arXiv preprint arXiv:1511.04944},
year={2015}
}

We are preparing an updated version of the paper. Stay tuned!

• For paper-related inquires, please contact authors of the paper.
• For code-related issues, please create a new issue or contact Gyuwan Kim (@kgwmath)