Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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.

Sanger Sequencing

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...

Protein Complex Assembly

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...

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....

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Hash functions in nucleotide sequence analysis.

Genome research·2026

Same authorSame journal

Estimation of substitution and indel rates via <i>k</i>-mer statistics.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2026

Same authorSame journal

A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2026

Same author

Efficiency of Learned Indexes on Genome Spectra.

LIPIcs : Leibniz international proceedings in informatics·2026

Same author

The gift of novelty: repeat-robust <i>k</i>-mer-based estimators of mutation rates.

bioRxiv : the preprint server for biology·2026

Same author

Data Structures to Represent a Set of <math><mi>k</mi></math> -long DNA Sequences.

ACM computing surveys·2026

Same journal

An Efficient Data Structure and Algorithm for Long-Match Query in Run-Length Compressed BWT.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2026

Same journal

Haplotype Threading Using the Positional Burrows-Wheeler Transform.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2026

Same journal

Acceleration of FM-index Queries Through Prefix-free Parsing.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2025

Same journal

PLA-index: A <i>k</i>-mer Index Exploiting Rank Curve Linearity.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2025

See all related articles

Search research articles

Related Experiment Video

Updated: May 9, 2025

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

Applying the Safe-And-Complete Framework to Practical Genome Assembly.

Sebastian Schmidt¹, Santeri Toivonen¹, Paul Medvedev^2,3

¹Department of Computer Science, University of Helsinki, Finland.

Algorithms in Bioinformatics : ... International Workshop, WABI ..., Proceedings. WABI (Workshop)

|April 29, 2025

Summary

This summary is machine-generated.

This study bridges genome assembly theory and practice by introducing simple omnitigs to improve contiguity. Modified assemblers show substantial gains with minimal computational cost and few misassemblies.

Keywords:

Applied computing → Computational biology Assembly evaluation Genome assembly HiFi sequencing data Mathematics of computing → Paths and connectivity problems Omnitigs Safe-and-complete framework Theory of computation → Graph algorithms analysis graph algorithm

More Related Videos

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Related Experiment Videos

Last Updated: May 9, 2025

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

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

A significant gap exists between theoretical genome assembly frameworks and practical software implementations.
Existing practical assemblers often lack theoretical accuracy guarantees, while theoretical algorithms are not widely adopted due to complexity or data limitations.

Purpose of the Study:

To bridge the gap between theoretical and practical genome assembly.
To improve contiguity in genome assemblies by integrating theoretical concepts into existing software.
To develop and evaluate an efficient algorithm for computing simple omnitigs and demonstrate their utility.

Main Methods:

The study proposes integrating the theoretical safe-and-complete framework into existing assemblers.
A simplified notion of omnitigs, termed 'simple omnitigs', was developed with an efficient computation algorithm.
Two assemblers, wtdbg2 and Flye, were modified by replacing their unitig algorithms with the simple omnitig algorithm.
Modifications were tested using real HiFi sequencing data from *D. melanogaster* and *C. elegans* genomes.

Main Results:

Modified assemblers demonstrated substantial improvements in alignment-based contiguity.
The integration of simple omnitigs incurred negligible additional computational costs.
The number of misassemblies showed either no increase or only a small increase.

Conclusions:

Simple omnitigs offer a practical approach to enhance genome assembly contiguity.
The modified assemblers provide a robust and efficient method for improving genome assembly quality.
This work successfully integrates theoretical advancements into practical bioinformatics tools.