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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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.
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Maxam-Gilbert Sequencing01:05

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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.
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Sanger Sequencing01:57

Sanger Sequencing

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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...
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RNA-seq03:21

RNA-seq

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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. 
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PCR01:32

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RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific...
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Updated: Jun 24, 2025

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

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MultiPrime: A reliable and efficient tool for targeted next-generation sequencing.

Han Xia1,2,3, Zhe Zhang4, Chen Luo3

  • 1School of Automation Science and Engineering, Faculty of Electronic and Information Engineering Xi'an Jiaotong University Xi'an China.

Imeta
|June 13, 2024
PubMed
Summary
This summary is machine-generated.

MultiPrime is a new tool that designs optimal primer sets for next-generation sequencing. It improves primer coverage and specificity, outperforming existing methods for viral detection.

Keywords:
degenerate primer designminimal primer setmultiplex PCRtargeted next‐generation sequencing

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Area of Science:

  • Bioinformatics
  • Molecular Biology
  • Genomics

Background:

  • Primer design is crucial for targeted sequencing.
  • Existing tools may lack efficiency and specificity for complex samples like microbiomes.
  • Next-generation sequencing (NGS) requires robust primer design for accurate results.

Purpose of the Study:

  • To introduce multiPrime, an automated tool for designing minimal primer sets for targeted NGS.
  • To enhance primer coverage, compatibility, and specificity, especially for microbiome and gene targets.
  • To evaluate multiPrime's performance against conventional primer design tools.

Main Methods:

  • MultiPrime automatically designs primer sets with mismatch tolerance for enhanced coverage.
  • Performance was evaluated using a dataset of 43,016 viral sequences.
  • The tool's application was expanded to 30 virus types and validated in 80 clinical specimens.

Main Results:

  • MultiPrime outperformed conventional primer design tools in performance evaluations.
  • Primer sets designed by multiPrime successfully amplified target amplicons.
  • Clinical validation demonstrated a sensitivity of 94% and a specificity of 89% for multiPrime-designed primers.

Conclusions:

  • MultiPrime is an effective tool for designing minimal primer sets for targeted NGS.
  • The tool offers improved coverage, compatibility, and specificity compared to existing methods.
  • MultiPrime shows high efficacy in viral detection applications, including clinical settings.