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Genome Annotation and Assembly

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 Sequencing

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.

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Improving Translational Accuracy

Improving Translational Accuracy

Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...

Maxam-Gilbert Sequencing

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.
Challenges of the Maxam-Gilbert Method
The...

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Related Experiment Video

Updated: May 21, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

SEQuel: improving the accuracy of genome assemblies.

Roy Ronen¹, Christina Boucher, Hamidreza Chitsaz

¹Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.

Bioinformatics (Oxford, England)

|June 13, 2012

Summary

This summary is machine-generated.

SEQuel corrects errors in next-generation sequencing assemblies, significantly reducing insertions, deletions, and substitutions. This tool improves both standard and challenging single-cell genome assemblies.

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Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

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Last Updated: May 21, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics

Background:

Next-generation sequencing (NGS) data assemblies contain errors post-assembly.
Error correction is crucial for accurate genomic data interpretation.

Purpose of the Study:

To develop SEQuel, a computational tool for correcting errors in assembled NGS contigs.
To improve the accuracy of both standard and single-cell genome assemblies.

Main Methods:

Utilizes a positional de Bruijn graph to model k-mers and read positions.
Applies a post-processing correction step to existing NGS assemblers.

Main Results:

SEQuel halved small insertions and deletions in multi-cell E. coli assemblies.
Corrected 30-94% of substitution errors and over 50% of indels in single-cell assemblies.
Refined the Deltaproteobacterium SAR324 single-cell genome assembly with over 800 corrections.

Conclusions:

SEQuel effectively corrects various errors in NGS assemblies.
The tool is vital for enhancing challenging single-cell genome assembly accuracy.
SEQuel is compatible with any NGS assembler and publicly available.