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Related Concept Videos

RNA-seq03:21

RNA-seq

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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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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Maxam-Gilbert Sequencing

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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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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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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3' End Sequencing Library Preparation with A-seq2
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3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

Assembly algorithms for deep sequencing data: basics and pitfalls.

Nitzan Kol1, Noam Shomron

  • 1Functional Genomics Laboratory, Tel Aviv University, Tel Aviv, Israel.

Methods in Molecular Biology (Clifton, N.J.)
|July 23, 2013
PubMed
Summary
This summary is machine-generated.

Genomic sequencing yields short DNA fragments, making genome assembly challenging. This chapter explains assembly difficulties and future expectations for reconstructing large DNA fragments.

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Last Updated: May 9, 2026

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Current genomic sequencing technologies produce limited read lengths, generating short DNA fragments.
  • Assembling these short fragments into a complete genome reconstruction is a significant computational challenge.

Purpose of the Study:

  • To elucidate the inherent difficulties in the genome assembly process.
  • To explore potential future advancements that may improve assembly outcomes.
  • To set realistic expectations for researchers regarding current genome assembly capabilities.

Main Methods:

  • This chapter provides a conceptual overview and theoretical explanation of the genome assembly problem.
  • It reviews existing challenges and limitations in current assembly algorithms and tools.

Main Results:

  • The inherent complexity of genome assembly stems from the nature of short-read sequencing data.
  • Despite extensive research and available tools, achieving perfect genome reconstruction remains difficult.

Conclusions:

  • Understanding the limitations of genome assembly is crucial for experimental design and data interpretation.
  • Future research directions hold promise for improving the accuracy and contiguity of genome assemblies.
  • Researchers should have realistic expectations about the scope and quality of results from current genome assembly experiments.