Моделирование первичных данных одномолекулярного секвенатора. Ч. 2. Симуляция последовательности событий встраивания меченых нуклеотидов в цепь ДНК и полноформатное моделирование изображений множества волноводов нулевой моды

Modeling of raw data from a single-molecule sequencer. Part II. Simulation of the sequence of events of fluorescently labeled nucleotides’ incorporation into a DNA strand and comprehensive modeling of multiple zero‑mode waveguides images

The article discusses the characteristics of detecting fluorescence signals from labeled nucleotides in a zero-mode waveguide (ZMW). It introduces the concept of a "signal event" to describe a single emission act in one of the spectral channels during the incorporation of a labeled nucleotide. The model accounts for label fluorescence duration, the formation of signal event sequences, and the background intervals between them. The moments of signal occurrence are modeled as a stationary one-dimensional Poisson process, characterized by properties such as discrete countability, stationarity, and orderliness. The article emphasizes the necessity of employing non-stationary models or combinations of processes when considering epigenetic effects, such as methylation. Finally, the article presents a software simulator for primary data acquisition in a third-generation single-molecule sequencer. This software generates output in FASTA, "movie," and "trace" formats, enabling the creation of image series that simulate the fluorescent array of zero-mode waveguides in a measurement cell.