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

You might also read

Related Articles

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

Sort by

Same author

Constancy of olfactory cilia in rodents.

Chemical senses·2025

Same author

Sulfur-doping gradient modulates spin-orbital engineering in cobalt single-atom catalysts: Optimized d-p orbital hybridization for efficient peroxymonosulfate activation.

Water research·2025

Same author

Genome-wide Association Studies of over 30,000 Samples with Bone Mineral Density at Multiple Skeletal Sites and Its Clinical Relevance.

Genomics, proteomics & bioinformatics·2025

Same author

Injectable Hydrogel Adhesive with Rapid In Situ Gelation and Robust Tissue Adhesion for Emergency Hemorrhage Control.

ACS applied materials & interfaces·2025

Same author

2025 ICM: Diagnostic Imaging for Periprosthetic Joint Infection.

The Journal of arthroplasty·2025

Same author

Comparative short- and long-term outcomes of TOETVA, ETGUA, and COT in thyroid cancer: a propensity score-matched study.

Frontiers in oncology·2025

Search research articles

Related Experiment Video

Updated: May 11, 2026

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA.

Daniel H Huson¹, Chao Xie

¹Singapore Centre on Environmental Life Sciences Engineering, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany and Life Sciences Institute, National University of Singapore, Singapore 117456.

Bioinformatics (Oxford, England)

|May 10, 2013

Summary

We developed PAUDA, a new metagenomic protein database search tool. It is ~10,000 times faster than BLASTX, offering comparable functional profiles for microbial community analysis.

More Related Videos

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Related Experiment Videos

Last Updated: May 11, 2026

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

A Clinical Metaproteomics Workflow Implemented within Galaxy Bioinformatics Platform to Analyze Host-Microbiome Interactions Underlying Human Disease

Published on: January 10, 2025

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Mass Spectrometry-Based Proteomics Analyses Using the OpenProt Database to Unveil Novel Proteins Translated from Non-Canonical Open Reading Frames

Published on: April 11, 2019

Area of Science:

Metagenomics
Bioinformatics
Computational Biology

Background:

Metagenomic data analysis relies on efficient protein database searching.
Existing tools like BLASTX can be computationally intensive for large datasets.
Accurate functional profiling is crucial for understanding microbial communities.

Purpose of the Study:

To introduce PAUDA, a novel and significantly faster protein database search approach for metagenomics.
To evaluate PAUDA's performance against established methods like BLASTX in terms of speed and accuracy.
To demonstrate PAUDA's utility in analyzing large-scale metagenomic datasets, such as permafrost soil samples.

Main Methods:

Development of the PAUDA (Protein Assignment Using a Database Approach) algorithm.
Comparative analysis of PAUDA and BLASTX on large-scale metagenomic datasets.
Assessment of read assignment rates to KEGG orthology groups.
Generation and comparison of gene and taxon abundance profiles.
Evaluation of sample clustering based on functional profiles.

Main Results:

PAUDA achieves a speed increase of approximately 10,000 times compared to BLASTX.
PAUDA shows a high correlation in gene and taxon abundance profiles with BLASTX.
The assignment rate of reads to KEGG orthology groups is approximately one-third of that achieved by BLASTX.
PAUDA analyzed 246 million reads in <80 CPU hours, whereas a similar BLASTX analysis required 800,000 CPU hours.
Functional profiles generated by PAUDA resulted in the same sample clustering as BLASTX.

Conclusions:

PAUDA offers a highly efficient alternative for protein database searching in metagenomics.
Despite a lower assignment rate, PAUDA provides comparable functional insights and sample classifications.
The computational efficiency of PAUDA enables the analysis of massive metagenomic datasets.
PAUDA is a valuable tool for advancing microbial community research through rapid functional profiling.