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.

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...

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.

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...

RNA-seq

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...

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...

You might also read

Related Articles

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

Sort by

Same author

Assembly of a high-quality reference genome for the rat tapeworm <i>Hymenolepis diminuta</i>.

bioRxiv : the preprint server for biology·2026

Same author

Intrinsic coordination of dynamic molecular signatures shape the human prefrontal cortex.

bioRxiv : the preprint server for biology·2026

Same author

An integrative single-nucleus multiomic atlas of the human left ventricle identifies gene regulatory network dynamics across cardiac development, aging, and disease.

Genome biology·2026

Same author

Author Correction: Single-cell atlas of the transcriptome and chromatin accessibility in the human retina.

Nature genetics·2026

Same author

Single-cell atlas of the transcriptome and chromatin accessibility in the human retina.

Nature genetics·2026

Same author

Standardizing RNA-seq Analysis of Fungal Pathogens Using BRC-Analytics and Agentic AI: A <i>Candidozyma auris</i> Case Study.

bioRxiv : the preprint server for biology·2026

Search research articles

Related Experiment Video

Updated: Jun 4, 2026

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Published on: August 27, 2014

Annotating genes and genomes with DNA sequences extracted from biomedical articles.

Maximilian Haeussler¹, Martin Gerner, Casey M Bergman

¹Faculty of Life Sciences, University of Manchester, Manchester, UK. maximilianh@gmail.com

Bioinformatics (Oxford, England)

|February 18, 2011

Summary

A new text-mining tool, text2genome, extracts DNA sequences from over 150,000 articles, accurately mapping them to genes and genomes. This facilitates genomic data analysis and publication discovery.

More Related Videos

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Related Experiment Videos

Last Updated: Jun 4, 2026

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Collection and Extraction of Saliva DNA for Next Generation Sequencing

Published on: August 27, 2014

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

The rapid increase in scientific publications and DNA sequencing data presents challenges for identifying relevant research on specific genes or genomic regions.
Current text-mining methods often rely on gene names, which can be ambiguous and lack precise genomic localization.

Purpose of the Study:

To develop and evaluate a novel text-mining approach for extracting DNA sequences from biomedical literature.
To automatically map these extracted sequences to genomic databases for precise gene and location identification.

Main Methods:

Extraction of DNA sequences directly from the text of open-access articles in PubMed Central (PMC).
Automated mapping of extracted DNA sequences to established genomic databases.
Validation of mapping accuracy at both the gene and genome levels.

Main Results:

Approximately 20% of open-access PMC articles contain extractable DNA sequences.
The developed method achieved high accuracy in mapping sequences to the correct gene (91%) and genome (96%).
Demonstrated utility of text2genome for interpreting ChIP-seq data and designing quantitative reverse transcriptase (RT)-PCR experiments.

Conclusions:

The text2genome approach successfully links research articles to genes and organisms without relying on potentially ambiguous gene names or identifiers.
This method generates genome annotation tracks from the biomedical literature.
Researchers can leverage modern genome browsers to analyze publications within the context of genomic data, enhancing discovery and interpretation.