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

Search research articles

Related Experiment Video

Updated: Jun 26, 2025

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Indexing and searching petabase-scale nucleotide resources.

Sergey A Shiryev¹, Richa Agarwala²

¹Department of Health and Human Services, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

|May 16, 2024

Summary

This summary is machine-generated.

Related Concept Videos

Nucleic Acids and Nucleotides

Nucleic Acids and Nucleotides

Nucleic acids are the most important macromolecules for the continuity of life. They carry the cell's genetic blueprint and have instructions for its functioning. The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA).
Deoxyribonucleic Acid (DNA)
DNA is the genetic material in all living organisms, ranging from single-celled bacteria to multicellular mammals. It is in the nucleus of eukaryotes and the organelles such as chloroplasts and mitochondria....

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key...

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...

You might also read

Related Articles

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

Sort by

Same author

dTOURS: Dense-region tagging for outbreak detection using ratio statistics.

PloS one·2025

Same author

SAUTE: sequence assembly using target enrichment.

BMC bioinformatics·2021

Same author

SKESA: strategic k-mer extension for scrupulous assemblies.

Genome biology·2018

Same journal

A comprehensive benchmark of sequence-based subcellular localization predictors for human proteins.

Nature methods·2026

Same journal

Efficient evidence-based genome annotation with EviAnn.

Nature methods·2026

Same journal

ClairS: a deep-learning method for long-read tumor-normal pair somatic small variant calling.

Nature methods·2026

Same journal

RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.

Nature methods·2026

Same journal

Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution.

Nature methods·2026

Same journal

EasyGrid: a versatile platform for automated cryo-EM sample preparation and quality control.

Nature methods·2026

See all related articles

Pebblescout is a new tool that makes searching large nucleotide sequence databases practical for researchers. It efficiently indexes and searches massive datasets, significantly reducing analysis time and effort.

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Vast nucleotide sequence data in resources like the Sequence Read Archive and GenBank are difficult to search.
Current methods are impractical for most researchers to navigate large-scale genomic data.

Purpose of the Study:

To introduce Pebblescout, a novel tool for indexing and searching large nucleotide sequence resources.
To enable efficient navigation and retrieval of relevant data from massive genomic datasets.

Main Methods:

Pebblescout employs dense sampling for indexing nucleotide sequences.
Search functionality identifies relevant runs or assemblies based on short sequence matches.
Results are ranked by the informativeness of the matches, providing well-defined guarantees.

More Related Videos

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

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

Related Experiment Videos

Last Updated: Jun 26, 2025

Pattern-based Search of Epigenomic Data Using GeNemo

Pattern-based Search of Epigenomic Data Using GeNemo

Published on: October 8, 2017

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

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

Main Results:

Eight databases indexing over 3.7 petabases were created using Pebblescout.
The tool effectively finds relevant subsets of large nucleotide resources across various query lengths.
Pebblescout demonstrates favorable performance compared to existing tools like MetaGraph and Sourmash.

Conclusions:

Pebblescout significantly reduces the effort required for downstream analysis of large nucleotide resources.
The tool offers a data-driven approach for efficient exploration of massive genomic data.
Pebblescout provides a practical solution for researchers dealing with rapidly growing sequence databases.