Abstract
Mining and analyzing the information and structure of DNA sequences is an important method of exploring and explaining the mysteries of biology. In addition to traditional biological detection methods for DNA sequences, technological advances have allowed researchers to utilize computers to analyze DNA sequences, such as in DNA visualization. However, DNA visualization techniques have disadvantages, such as difficult operation and complex calculation. Therefore, in this paper, we propose an algorithm called VARCH based on a variant map that is a part of variant logic construction. VARCH is a high-efficiency and concise visualization algorithm for DNA sequences. The principle of this approach is that the number of base combinations in each DNA subsequence is counted, and a matrix is constructed based on the full arrangement of different base combinations. Finally, the matrix is mapped to the 2D coordinate plane, obtaining the image of DNA sequences. The experimental results demonstrate that VARCH can effectively display features of DNA sequences.
Highlights
PRINCIPLE OF VARCH we present the motivation of VARCH by explaining how to visualize DNA sequences based on Variant logic construction (VLC)
WORK In this study, we propose a new 2D graphical representation of DNA sequences called VARCH, which is based on variant logic construction
The principle of VARCH is that the bases in the DNA sequence are replaced with four meta operators in the variant logic construction
Summary
In Earth’s long history, a number of species have existed, some of which have disappeared and some of which have survived to this day. Since Hamori and Ruskin [6] initially proposed using the H-curve to graph DNA sequences in 1983, an increasing number of visualization methods have been proposed [7]–[9] These methods include 2D space [10], 3D space [11], and higher-dimensional spaces, such as 4D [12], 5D [13], and 6D spaces [14]. In this study we propose a new method for the visual analysis of DNA sequences based on variant logic construction called VARCH [15]–[17]. This method can help people observe the DNA sequence more intuitively, especially for non-biological researchers, and the feature of the DNA sequence becomes more be found.
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