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Next-generation Sequencing03:00

Next-generation Sequencing

95.4K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.8K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
11.8K
Sanger Sequencing01:57

Sanger Sequencing

765.1K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
765.1K
RNA-seq03:21

RNA-seq

10.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.9K
Homologous Recombination02:31

Homologous Recombination

58.4K
The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
58.4K
DNA Isolation01:24

DNA Isolation

43.1K
DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...
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Related Experiment Video

Updated: Nov 9, 2025

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

8.9K

QuASeR: Quantum Accelerated de novo DNA sequence reconstruction.

Aritra Sarkar1, Zaid Al-Ars1, Koen Bertels2

  • 1Department of Quantum and Computer Engineering, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

Plos One
|April 12, 2021
PubMed
Summary
This summary is machine-generated.

We introduce QuASeR, a novel quantum computation method for DNA sequence reconstruction using de novo assembly. This tool aids genomics research by enabling efficient DNA sequence assembly on quantum platforms.

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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Area of Science:

  • Bioinformatics
  • Quantum Computing
  • Genomics

Background:

  • De novo assembly is crucial for reconstructing genomes from short DNA reads.
  • Current assembly methods face challenges with scalability and accuracy.
  • Quantum computing offers potential for novel computational approaches in bioinformatics.

Purpose of the Study:

  • To present QuASeR, a reference-free DNA sequence reconstruction implementation.
  • To demonstrate the application of quantum computation for de novo DNA assembly.
  • To provide a self-contained explanation for genomics researchers and quantum developers.

Main Methods:

  • Modeling DNA sequence reconstruction using quantum computation.
  • Implementing the algorithm using four key steps: Traveling Salesperson Problem (TSP), Quadratic Unconstrained Binary Optimization (QUBO), Hamiltonians, and Quantum Approximate Optimization Algorithm (QAOA).
  • Executing the algorithm on gate-based quantum simulators, D-Wave quantum annealing simulators, and hardware.

Main Results:

  • Successful reconstruction of DNA sequences from DNA reads using QuASeR.
  • Demonstration of proof-of-concept for each implementation step.
  • Analysis of performance on both quantum simulators and hardware.

Conclusions:

  • QuASeR represents the first quantum computation model for reference-free DNA sequence reconstruction.
  • The study highlights the potential and limitations of current quantum systems for bioinformatics applications.
  • The open-source implementation facilitates further research and development in quantum bioinformatics.