References

Atomic Number

Reference used for the atomic number encoding:

Kwan, Hon Keung, and Swarna Bai Arniker. "Numerical representation of DNA sequences." 2009 IEEE International Conference on Electro/Information Technology. IEEE, 2009.

Chaos Game

Reference used for the Chaos Game representation encoding:

Jeffrey, H. Joel. "Chaos game representation of gene structure." Nucleic acids research 18.8 (1990): 2163-2170.

Cross

The cross encoding is inspired by the complex number encoding / QPSK encoding described in:

Chakravarthy, Niranjan, et al. "Autoregressive modeling and feature analysis of DNA sequences." EURASIP Journal on Advances in Signal Processing 2004 (2004): 1-16.

DNA Walk

Reference used for the DNA walk encoding:

Hewelt, Blake, et al. "The DNA walk and its demonstration of deterministic chaos—relevance to genomic alterations in lung cancer." Bioinformatics 35.16 (2019): 2738-2748.

EIIP

Reference used for the electron-ion interaction pseudopotential encoding:

Nair, Achuthsankar S., and Sivarama Pillai Sreenadhan. "A coding measure scheme employing electron-ion interaction pseudopotential (EIIP)." Bioinformation 1.6 (2006): 197.

Fickett Score

Reference used for the Fickett score:

Fickett, James W. "Recognition of protein coding regions in DNA sequences." Nucleic acids research 10.17 (1982): 5303-5318.

Onehot (Voss)

Reference used for the Onehot (Voss) encoding:

Kwan, Hon Keung, and Swarna Bai Arniker. "Numerical representation of DNA sequences." 2009 IEEE International Conference on Electro/Information Technology. IEEE, 2009.

Real-number (PAM)

Reference used for the real-number encoding:

Chakravarthy, Niranjan, et al. "Autoregressive modeling and feature analysis of DNA sequences." EURASIP Journal on Advances in Signal Processing 2004 (2004): 1-16.

TF-IDF

Reference used for TF-IDF encoding:

Salton, Gerard, and Christopher Buckley. "Term-weighting approaches in automatic text retrieval." Information processing & management 24.5 (1988): 513-523.

Z-Curve

Reference used for the Z-curve encoding:

Zhang, Ren, and Chun-Ting Zhang. "A brief review: The z-curve theory and its application in genome analysis." Current genomics 15.2 (2014): 78-94.