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

You might also read

Related Articles

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

Sort by
Same author

HeartBioPortal 3.0: an integrated cardiovascular genomics knowledge environment for molecular, clinical and population-scale interpretation.

medRxiv : the preprint server for health sciences·2026
Same author

Current trends and challenges in deciphering single molecule resolution maps of single cell transcriptomes.

Briefings in bioinformatics·2026
Same author

Regulation Ratio: A Singular Multi-Omic Measurement of Gene Regulatory Mechanisms.

Computational and structural biotechnology journal·2026
Same author

Single-Cell Transcriptomic Analysis of Salivary Epithelial Cells Reveals Large-Scale Dysregulation in Bitter Taste Dysfunction.

International journal of molecular sciences·2026
Same author

Genotype-Based Severity Scoring System in Wolfram Syndrome: Correlation with Onset of Cardinal Symptoms and <i>WFS1</i> Gene Variant Types.

medRxiv : the preprint server for health sciences·2026
Same author

BigEye: a clinically interpretable deep learning framework for diabetic retinopathy detection and stage prediction.

Scientific reports·2026

Related Experiment Video

Updated: Oct 29, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
07:33

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

31.0K

Sequoia: an interactive visual analytics platform for interpretation and feature extraction from nanopore sequencing

Ratanond Koonchanok1, Swapna Vidhur Daulatabad2, Quoseena Mir2

  • 1Department of Human-Centered Computing, School of Informatics and Computing, Indiana University Purdue University, 535 W Michigan St, Indianapolis, IN, 46202, USA.

BMC Genomics
|July 8, 2021
PubMed
Summary

Sequoia is a new visual analytics tool for exploring nanopore RNA sequencing data. It helps identify RNA modifications like m6A and m5C by clustering sequences and visualizing signal features.

Keywords:
BioinformaticsEpitranscriptomeNanopore signal analysisNext-generation-sequencingRNA modificationsSingle-Molecule SequencingVisual infrastructure

More Related Videos

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.4K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.1K

Related Experiment Videos

Last Updated: Oct 29, 2025

Nanopore DNA Sequencing for Metagenomic Soil Analysis
07:33

Nanopore DNA Sequencing for Metagenomic Soil Analysis

Published on: December 14, 2017

31.0K
Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

2.4K
Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example
05:45

Validating Whole Genome Nanopore Sequencing, using Usutu Virus as an Example

Published on: March 11, 2020

9.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Direct RNA sequencing offers long reads and single-molecule resolution for detecting post-transcriptional modifications.
  • New analytical tools are crucial for harnessing the potential of this RNA sequencing data.

Purpose of the Study:

  • To introduce Sequoia, an interactive visual analytics tool for nanopore RNA sequencing data.
  • To enable exploration of sequence data, clustering, and identification of RNA modification signals.

Main Methods:

  • Developed Sequoia with a Python backend and multi-view visualization interface.
  • Enabled import of raw nanopore sequencing data (Fast5 format).
  • Utilized electric-current similarities for sequence clustering and signal analysis.

Main Results:

  • Demonstrated Sequoia's application on ~500k reads from human HeLa cell line direct RNA sequencing data.
  • Successfully separated modified RNA sequences (m6A, m5C) from unmodified ones through visual exploration.
  • Identified novel signal signatures characterizing RNA modifications.

Conclusions:

  • Sequoia complements existing computational tools for nanopore RNA analysis.
  • Visual analysis aids in hypothesis generation and understanding RNA dynamics.
  • The tool is publicly available for researchers.