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

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Covalently Linked Protein Regulators

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....

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

Lime amendment to chronically acidified forest soils results in shifts in prokaryotic communities.

Applied and environmental microbiology·2025

Same author

Nitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph <i>Candidatus</i> Thalassolituus haligoni.

Science advances·2024

Same author

Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere.

Microbiome·2023

Same author

Gut bacterial gene changes following pegaspargase treatment in pediatric patients with acute lymphoblastic leukemia.

Leukemia & lymphoma·2021

Same author

A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere.

Microbiome·2021

Same author

Identifying biases and their potential solutions in human microbiome studies.

Microbiome·2021

Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026

Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026

Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026

Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026

Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026

Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: May 23, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2.

Robyn J Wright¹, Morgan G I Langille¹

¹Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada.

Bioinformatics (Oxford, England)

|April 28, 2025

Summary

This summary is machine-generated.

An updated PICRUSt2 database (PICRUSt2-SC) significantly expands microbial genome representation and functional annotations for amplicon sequencing data. This streamlined database improves the accuracy of microbial function predictions across diverse environments.

More Related Videos

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Related Experiment Videos

Last Updated: May 23, 2025

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Author Spotlight: A Computational Approach to Decipher Amino Acid Preferences in Multispecific Protein-Protein Interactions

Published on: January 26, 2024

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Microbial genomics
Bioinformatics
Metagenomics

Background:

PICRUSt2 is a key bioinformatic tool for predicting microbial community functions from amplicon sequencing data.
The accuracy of PICRUSt2 predictions relies heavily on the comprehensiveness and annotation quality of its reference genome database.
Previous PICRUSt2 database updates were hindered by manual, time-consuming, and computationally intensive processes.

Purpose of the Study:

To develop and implement an updated, more comprehensive database for PICRUSt2.
To streamline the database update process for regular, ongoing improvements.
To enhance the accuracy of microbial function prediction by improving environmental representation within the database.

Main Methods:

Constructed an updated PICRUSt2 database (PICRUSt2-SC) by substantially increasing the number of bacterial and archaeal genomes.
Developed a new, streamlined process for regular database upgrades, replacing previous manual methods.
Validated the improved database by assessing genome representation and its impact on functional prediction accuracy.

Main Results:

The PICRUSt2-SC database significantly increased bacterial genomes from 19,493 to 26,868 and archaeal genomes from 406 to 1,002.
The new database incorporates a greater number of functional annotations compared to previous versions.
Genomes within the PICRUSt2-SC database demonstrate closer matches to study sequences from various environments, enhancing predictive accuracy.

Conclusions:

The PICRUSt2-SC database offers a substantial improvement over previous versions, providing better microbial genome representation and functional annotations.
The streamlined update process facilitates ongoing maintenance and improvement of the PICRUSt2 database.
Enhanced environmental representation in the PICRUSt2-SC database leads to more accurate microbial function predictions from amplicon sequencing data.