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

Ribosome Profiling

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...

Gene Evolution - Fast or Slow?

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

Modern Molecular Taxonomy

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...

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...

Ribosomal RNA Synthesis

Ribosomal RNA Synthesis

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

Orobas: A computational approach for scoring and analysis of quantitative chemical-genetic interactions from CRISPR-Cas9 screens.

STAR protocols·2026

Same author

Global genetic interaction network of a human cell maps conserved principles and informs functional interpretation of gene co-essentiality profiles.

Cell·2026

Same author

Longitudinal gut microbiome dynamics are associated with clinical outcome and toxicity during ibrutinib therapy.

Gut microbes·2026

Same author

Expanding TheCellMap.org to visualize a genome-scale genetic interaction network for a human cell line.

bioRxiv : the preprint server for biology·2026

Same author

Identification of a robust metabolic signature associated with hospital-acquired pneumonia and response to interferon-gamma treatment in critically ill patients.

Critical care (London, England)·2026

Same author

Morphine Plus Placebo vs Morphine Plus Acetaminophen for Acute Pain in the Emergency Department: A Randomized Clinical Trial.

JAMA network open·2026

Search research articles

Related Experiment Video

Updated: Mar 26, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

NINJA-OPS: Fast Accurate Marker Gene Alignment Using Concatenated Ribosomes.

Gabriel A Al-Ghalith¹, Emmanuel Montassier^2,3, Henry N Ward⁴

¹Biomedical Informatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, United States of America.

Plos Computational Biology

|January 29, 2016

Summary

NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS) is a novel bioinformatics tool for fast and accurate microbial marker gene matching. It significantly speeds up operational taxonomic unit (OTU) picking for microbiome studies.

More Related Videos

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Related Experiment Videos

Last Updated: Mar 26, 2026

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons

Published on: August 29, 2014

Area of Science:

Bioinformatics
Computational Biology
Microbiome Research

Background:

Next-generation sequencing (NGS) generates vast amounts of short-read genomics data.
Short-read mapping is crucial for assembling genomes and analyzing microbial communities.
Existing methods for microbial marker gene sequencing often rely on heuristic approaches.

Purpose of the Study:

To introduce NINJA Is Not Just Another OTU-Picking Solution (NINJA-OPS, or NINJA), a novel method for reference-based marker gene matching.
To provide a fast, accurate, and memory-efficient solution for operational taxonomic unit (OTU) picking.
To enable efficient analysis of microbiome data from short-read sequencing.

Main Methods:

NINJA utilizes Burrows-Wheeler (BW) alignment with a 'concatesome' (concatenated reference sequences) as input.
The method supports paired-end reads with variable insert sizes.
It incorporates pre-filtering techniques for enhanced speed and integrates with existing bioinformatics tools.

Main Results:

NINJA achieves accuracy comparable to or exceeding existing reference-based OTU-picking methods.
It demonstrates an order of magnitude or greater speedup in processing times.
The tool uses a significantly reduced memory footprint compared to previous methods.

Conclusions:

NINJA-OPS offers a highly efficient and accurate solution for reference-based OTU picking in microbiome studies.
The pipeline can process an entire MiSeq run of 16S rRNA gene data in under 10 minutes on standard hardware.
NINJA is a free, open-source tool that simplifies and accelerates microbiome data analysis.