• Base Pair: A base pair is two chemical bases bonded to one another forming part of the DNA double helix. The DNA molecule consists of two strands that wind around one another for the formation of the double helix structure. The four bases are adenine (A), thymine (T), guanine (G), and cytosine (C). A always pairs with T, and G always pairs with C, forming the base pairs.
• Sequencer: A sequencer is a scientific instrument used to automate the DNA sequencing process. DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA.
• DNA-to-Signal Mapping: This refers to the process of converting the sequence of nucleotides in a DNA molecule into a corresponding signal that can be processed and analyzed.
• Biophysical Assignment: This refers to the process of assigning numerical values to nucleotides based on their biophysical properties. Instead of simply identifying the nucleotides as A, G, C, or T, additional information can be captured by considering various physical or chemical properties of the nucleotides.
• Electron-Ion Interaction Potentials (EIIP): This is a measure of the energy level of electrons in a substance. In the context of DNA, it is a value assigned to each nucleotide based on its electron-ion interaction potential.
• DNA-Walk Model: In the DNA-walk model, a DNA sequence is represented as a path in a three-dimensional space. Each nucleotide is represented by a step in a particular direction.
• Z-Curve Representation: The Z-curve representation is another way to visualize DNA sequences. It is a three-dimensional curve that represents a DNA sequence by plotting three parameters against the sequence position.
• Single Atomic Numbers: This method assigns each nucleotide a single atomic number based on the atomic constituents of the base. For example, one might assign A, G, C, and T the atomic numbers of nitrogen (7), oxygen (8), phosphorus (15), and carbon (6), respectively.
• Paired Nucleotide Representations: This is a method of encoding where pairs of nucleotides are considered together, rather than individually. Each pair of nucleotides is assigned a unique representation, which can allow for more complex analyses of DNA sequences.
• DNA Properties: These are the physical and chemical characteristics of DNA molecules, such as their shape, size, electrical charge, and the physical and chemical properties of the nucleotides they contain. These properties can have significant effects on how DNA molecules interact with each other and with other molecules.
• Sampling Fidelity: This refers to the accuracy with which a sample represents the population from which it was drawn. In the context of DNA sequencing, it refers to the accuracy with which the sequenced DNA represents the original DNA sample.
• Arbitrary Symbol Based on Some Scheme: This is a method of encoding information where each piece of information (in this case, each nucleotide) is represented by an arbitrary symbol. The symbols can be based on any scheme, such as binary, integer, complex, or tetrahedral schemes.