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Related Concept Videos

Genomics02:02

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...
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...
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.
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.
Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...

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Related Experiment Video

Updated: Jun 25, 2026

Culturing of Human Nasal Epithelial Cells at the Air Liquid Interface
10:38

Culturing of Human Nasal Epithelial Cells at the Air Liquid Interface

Published on: October 8, 2013

37.6K

LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data.

Ahmed Al Qaffas1, Jenna Nichols2, Andrew J Davison2

  • 1Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, USA.

Virus Evolution
|May 17, 2021
PubMed
Summary
This summary is machine-generated.

A new tool called LoReTTA (Long Read Template-Targeted Assembler) improves viral genome assembly from long-read sequencing data. It outperforms existing methods in contiguity and accuracy for complex samples.

Keywords:
PacBiode novo assemblylong read assemblerviral genomics

Related Experiment Videos

Last Updated: Jun 25, 2026

Culturing of Human Nasal Epithelial Cells at the Air Liquid Interface
10:38

Culturing of Human Nasal Epithelial Cells at the Air Liquid Interface

Published on: October 8, 2013

37.6K

Area of Science:

  • Genomics and Bioinformatics
  • Molecular Biology
  • Virology

Background:

  • Long-read sequencing technologies offer advantages over short-read methods for assembling large genomes.
  • Existing short-read assembly tools are inadequate for long-read data due to differences in read length and error rates.
  • Viral genomes present unique challenges for assembly, including high genetic variability and potential co-infections.

Purpose of the Study:

  • To develop a novel bioinformatics tool for de novo assembly of long-read sequencing data from viral genomes.
  • To create a tool, LoReTTA (Long Read Template-Targeted Assembler), that leverages reference genomes to guide assembly.
  • To address the specific challenges of assembling viral genomes from complex clinical or environmental samples.

Main Methods:

  • Development of LoReTTA, a long-read assembler specifically designed for viral genomes.
  • Utilization of a reference-guided assembly approach, adapted for long reads.
  • Testing and validation using simulated and experimental datasets from the PacBio platform.

Main Results:

  • LoReTTA demonstrated superior performance compared to established long-read assemblers.
  • The tool achieved higher contiguity and accuracy in viral genome assembly.
  • Successful assembly of viral genomes from datasets with high genetic variability and mixed organisms.

Conclusions:

  • LoReTTA is an effective tool for accurate and contiguous de novo assembly of long-read viral genome data.
  • The reference-guided approach is beneficial for assembling challenging viral genomes.
  • The software is user-friendly, adaptable, and readily available for the scientific community.