Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
Although bacterial genomes are much...
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.
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...

You might also read

Related Articles

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

Sort by
Same author

Spatiotemporal expression of endospore appendages and cryo-EM insights into Ena1C-mediated S-ENA anchoring in Bacillus paranthracis.

Scientific reports·2026
Same author

Synthesis and Antimicrobial Specificities of Halogenated Tryptophan-Containing Nisin Variants.

ACS chemical biology·2025
Same author

Functionalizing Nisin with a Sugar Moiety Improves Its Solubility and Results in an Altered Antibacterial Spectrum and Mode of Action.

ACS synthetic biology·2025
Same author

Insight into the epigenetic regulation of gene expression in the bloodstream and procyclic forms of <i>Trypanosoma brucei</i> through the involvement of G-quadruplexes.

NAR genomics and bioinformatics·2025
Same author

Design and Biosynthesis of Ornithine 8-Containing Semaglutide Variants with a Click Chemistry-Modifiable Position 26.

ACS synthetic biology·2025
Same author

FLINT: Learning-Based Flow Estimation and Temporal Interpolation for Scientific Ensemble Visualization.

IEEE transactions on visualization and computer graphics·2025

Related Experiment Video

Updated: Jun 28, 2026

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

Prosecutor: parameter-free inference of gene function for prokaryotes using DNA microarray data, genomic context and

Evert Jan Blom1, Rainer Breitling, Klaas Jan Hofstede

  • 1Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, the Netherlands. e.j.blom@rug.nl

BMC Genomics
|October 23, 2008
PubMed
Summary

Researchers can now predict gene function using the Prosecutor application, which leverages gene expression data and biological information for rapid, large-scale analysis. This tool aids in understanding gene roles across 11 prokaryotic organisms.

More Related Videos

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Related Experiment Videos

Last Updated: Jun 28, 2026

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae
10:18

A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
08:07

Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions

Published on: August 2, 2015

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Functional genomic studies have identified many genes, but their specific functions remain largely unknown.
  • The guilt-by-association principle, using similar gene expression patterns, offers a method for large-scale function prediction.
  • Microarray data availability facilitates the application of guilt-by-association for inferring gene roles.

Purpose of the Study:

  • To develop a computational tool, Prosecutor, for rapid gene function inference.
  • To enable researchers to predict gene function using gene expression data and functional annotations.
  • To enhance function prediction by incorporating genomic context and prokaryotic-specific regulatory mechanisms.

Main Methods:

  • Developed Prosecutor, a parameter-free application for gene function prediction.
  • Employed a sensitive algorithm to link genes with unknown functions to annotated genes.
  • Integrated genomic context and known regulatory mechanisms specific to prokaryotes.

Main Results:

  • Prosecutor achieved a high association rate in linking genes with unknown functions to annotated genes.
  • Analyzed publicly available transcriptome datasets and validated predicted functions using literature sources.
  • Provided comprehensive analysis results for 11 prokaryotic organisms, accessible via a dedicated website.

Conclusions:

  • Prosecutor software and supplementary datasets facilitate rapid identification of putative gene functions for researchers.
  • The tool supports researchers working with 11 analyzed prokaryotic organisms.
  • The system allows for de novo analysis, enabling the study of new organisms.