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Single-Molecule Analysis by Biological Nanopores
Published in Shuo Huang, Single-Molecule Tools for Bioanalysis, 2022
Exosequencing has been demonstrated as a parallel alternative strategy for nanopore sequencing with a high-base calling accuracy. In this approach, an exonuclease is conjugated adjacent to the nanopore rim, and digests individual nucleotides from a DNA template to be sequenced. These nucleotides, when passing through the nanopore in sequence according to their cleavage order, can be sequentially identified [85–87]. Studies toward an exosequencing system show that four nucleoside monophosphates can be discriminated with an average accuracy up to 99.8% [87], as can the four ribonucleoside diphosphates [88]. However, it is hard to guarantee the order of the released nucleotides against the interference from stochastic diffusion.
Big Data and Transcriptomics
Published in Shampa Sen, Leonid Datta, Sayak Mitra, Machine Learning and IoT, 2018
Sudharsana Sundarrajan, Sajitha Lulu, Mohanapriya Arumugam
The raw sequence-based metrics checks the experiments at low-level as prior sequence alignments are not required. The raw sequence quality is assessed based on the Phred quality score (Q). Phred score measures the base-calling reliability from Sanger sequencing chromatograms. It is defined as Q = −10 × log10(P), where P is the probability of erroneous base calling. GC content gives the percentage of either guanine or cytosine bases in a DNA sequence. It is a simple way to measure the nucleotide composition. Read duplication is often determined by read length, transcript abundance, PCR amplification, and sequence depth.
Quantum technology a tool for sequencing of the ratio DSS/DNA modifications for the development of new DNA-binding proteins
Published in Egyptian Journal of Basic and Applied Sciences, 2022
Adamu Yunusa Ugya, Kamel Meguellati
In 2003, roughly US$3 billion was spent on DNA sequencing reagents and enzymes, as well as analyzer equipments and softwares for automated sequence determination. The Capillary electrophoresis (CE) method was used to determine the majority of the DNA sequencing output. Over the last ten years, this technology has been proportionately used to develop a faster technique. CE provides high resolution and throughput, automatic operation and data collection, and also online dye detection on DNA extension products. As the run advances operational advances like pulsed-field and graduated electric fields, as well as automated thermal ramping programs, result in higher base resolution and longer sequence reads. Advanced base-calling algorithms and DNA marker additives that use known fragment sizing landmarks can increase fragment base-calling by 20–30%, boosting call accuracy and read durations. Despite CE sequencers’ high efficiency, the complete delineation of the human genome and its implications for genome-wide analysis for personalized medicine are driving the development of devices and chemicals capable of massively increased sequence throughput. Miniaturization of CE into chip-based devices gives all of the above benefits, as well as a significant boost in analysis speed and automation. New array-based sequencing devices promise a quantum increase in efficiency [7].