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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.
Next-generation Sequencing03:00

Next-generation Sequencing

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.
RACE - Rapid Amplification of cDNA Ends02:35

RACE - Rapid Amplification of cDNA Ends

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 primer.
Since the...
Sanger Sequencing01:57

Sanger Sequencing

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

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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Related Experiment Video

Updated: Jun 6, 2026

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

PE-Assembler: de novo assembler using short paired-end reads.

Pramila Nuwantha Ariyaratne1, Wing-Kin Sung

  • 1Computational & Mathematical Biology Group, Genome Institute of Singapore, Singapore.

Bioinformatics (Oxford, England)
|December 15, 2010
PubMed
Summary

This study introduces a novel 3' extension method for de novo genome assembly, bypassing complex de bruijn graphs. This approach yields more contiguous, complete, and accurate genome assemblies compared to existing techniques.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • De novo genome assembly methods often rely on de bruijn graphs, which can be computationally intensive and difficult to parallelize.
  • Existing graph-based approaches may struggle with large genomes and subtle genomic information.

Purpose of the Study:

  • To develop a novel, massively parallelizable genome assembly method.
  • To overcome the limitations of traditional de bruijn graph-based assemblers.

Main Methods:

  • A new 3' extension approach for genome assembly is presented.
  • This method avoids the use of complex graph structures.

Main Results:

  • The proposed 3' extension method achieves more contiguous genome assemblies.
  • Assemblies generated are more complete and less error-prone than those from existing methods.
  • The approach demonstrates potential for massive parallelization.

Conclusions:

  • The 3' extension method offers a promising alternative to graph-based genome assembly.
  • This technique can lead to improved efficiency and accuracy in genomic data analysis.