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Related Concept Videos

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.
Maxam-Gilbert Sequencing01:05

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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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...
RNA-seq03:21

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Next-generation Sequencing

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Related Experiment Video

Updated: May 29, 2026

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles
10:23

Self-assembly of Complex Two-dimensional Shapes from Single-stranded DNA Tiles

Published on: May 8, 2015

An integer programming approach to DNA sequence assembly.

Youngjung Chang1, Nikolaos V Sahinidis

  • 1Department of Chemical Engineering, Carnegie Mellon University, Pittsburgh, PA, USA. yjchang@andrew.cmu.edu

Computational Biology and Chemistry
|August 26, 2011
PubMed
Summary
This summary is machine-generated.

This study presents a new method for DNA sequence assembly, crucial for DNA sequencing technologies. It efficiently finds all possible DNA sequences, improving accuracy and reliability in reconstructing genetic information.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • De novo sequence assembly is a fundamental challenge in DNA sequencing.
  • Errors in experimental data complicate assembly and may yield non-unique solutions.
  • Current heuristic methods often neglect the enumeration of all alternative reconstructions.

Purpose of the Study:

  • To develop a robust method for DNA sequence assembly with errors.
  • To enable the identification of all possible DNA sequence reconstructions.
  • To enhance the reliability of inferring the true DNA sequence.

Main Methods:

  • Integer programming formulation for sequence assembly.
  • Global optimization strategy for solving the assembly problem.
  • Efficient technique for enumerating alternative sequence reconstructions.

Main Results:

  • The developed approach significantly extends the length of DNA sequences that can be assembled with a global optimality certificate (over 10,000 bases).
  • The method successfully handles DNA sequencing data with experimental errors.
  • Alternative solutions were found to vary in their ability to reproduce the target DNA sequence.

Conclusions:

  • The proposed integer programming and global optimization strategy reliably identifies all alternative DNA sequence reconstructions.
  • Enumerating all solutions is critical for accurate DNA sequence inference, especially with noisy data.
  • This methodology enhances the reliability of DNA sequence reconstruction and can guide experimental design.