用整数混沌博弈表示编码DNA序列
Encoding DNA sequences by integer chaos game representation
摘要：
DNA序列是编码遗传信息的基础。遗传信息不仅可以通过符号序列来理解，还可以通过序列中隐藏的信号来理解。需要将符号序列转换为数字序列，以便通过信号处理技术揭示隐藏的信号。目前所有的转换方法都是将DNA序列编码为相同长度的数值。这些表示在基因组信号压缩、加密和隐写等应用中存在局限性。提出了一种DNA序列的整数混沌博弈表示（iCGR）和基于iCGR的DNA序列无损编码方法。在iCGR方法中，DNA序列由核苷酸及其在序列中的位置的迭代函数表示。然后，DNA序列可以被唯一地编码，并使用来自iCGR的三个整数来恢复。一个整数是序列长度，另外两个整数表示序列中核苷酸的累积分布。整数编码方案可以将DNA序列压缩每个核苷酸2位。DNA序列的整数表示为序列压缩、加密和隐写提供了一种有前景的工具。本研究中的Python程序可在https://github.com/cyinbox/iCGR上免费向公众提供
英文摘要：
DNA sequences are fundamental for encoding genetic information. The genetic information may not only be understood by symbolic sequences but also from the hidden signals inside the sequences. The symbolic sequences need to be transformed into numerical sequences so the hidden signals can be revealed by signal processing techniques. All current transformation methods encode DNA sequences into numerical values of the same length. These representations have limitations in the applications of genomic signal compression, encryption, and steganography. We propose an integer chaos game representation (iCGR) of DNA sequences and a lossless encoding method DNA sequences by the iCGR. In the iCGR method, a DNA sequence is represented by the iterated function of the nucleotides and their positions in the sequence. Then the DNA sequence can be uniquely encoded and recovered using three integers from iCGR. One integer is the sequence length and the other two integers represent the accumulated distributions of nucleotides in the sequence. The integer encoding scheme can compress a DNA sequence by 2 bits per nucleotide. The integer representation of DNA sequences provides a prospective tool for sequence compression, encryption, and steganography. The Python programs in this study are freely available to the public at https://github.com/cyinbox/iCGR
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