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

Peptide Identification Using Tandem Mass Spectrometry01:33

Peptide Identification Using Tandem Mass Spectrometry

7.7K
Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...
7.7K

You might also read

Related Articles

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

Sort by
Same author

Longitudinal multiomics profiling of extracorporeal cross-circulation with pig liver xenografts in human decedents.

Nature medicine·2026
Same author

Long-term clinical outcomes from the smart start trial: rituximab, lenalidomide and ibrutinib in patients with newly diagnosed large B-cell lymphoma.

Blood cancer journal·2026
Same author

A Patient-Derived Xenograft Repository Capturing Clinical and Molecular Heterogeneity of Large B-cell Lymphoma.

Blood cancer discovery·2026
Same author

Multiplexed cytokine and antigen mRNA administration generates durable anti-tumor immunity against pancreatic cancer.

Nature communications·2026
Same author

Zebrafish knock-in lines enabling live visualization of extracellular matrix dynamics during development and regeneration.

Development (Cambridge, England)·2026
Same author

Pathogenesis of diffuse large B cell lymphoma proteogenotypes.

Cancer cell·2026

Related Experiment Video

Updated: Dec 1, 2025

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

508

dagLogo: An R/Bioconductor package for identifying and visualizing differential amino acid group usage in proteomics

Jianhong Ou1,2, Haibo Liu1, Niraj K Nirala3

  • 1Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.

Plos One
|November 6, 2020
PubMed
Summary

The new dagLogo tool enhances protein motif identification by using reduced amino acid alphabets for better visualization and statistical analysis. It reveals biological patterns missed by other tools.

More Related Videos

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

4.7K
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.1K

Related Experiment Videos

Last Updated: Dec 1, 2025

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

508
An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA
07:55

An Optimized Quantitative Pull-Down Analysis of RNA-Binding Proteins Using Short Biotinylated RNA

Published on: February 17, 2023

4.7K
Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.1K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Molecular Biology

Background:

  • Sequence logos are standard for visualizing conserved nucleic acid and protein motifs.
  • Identifying and visualizing protein motifs is challenging due to amino acid alphabet complexity, post-translational modifications, and diverse protein localization.
  • Reduced amino acid alphabets aid in protein alignment, folding, structure prediction, and evolution studies, but tools for their application in motif identification are lacking.

Purpose of the Study:

  • To develop a versatile tool for identifying and visualizing statistically significant protein motifs using reduced amino acid alphabets.
  • To address the limitations of existing tools in handling diverse protein data and applying reduced amino acid representations.

Main Methods:

  • Development of the R/Bioconductor package dagLogo.
  • Implementation of various input formats and background model options.
  • Integration of different reduced amino acid alphabets to group amino acids by properties.
  • Inclusion of statistical and visual solutions for differential amino acid usage analysis.

Main Results:

  • dagLogo offers comprehensive options for input data and background models.
  • The package supports various reduced amino acid alphabets for grouping amino acids.
  • dagLogo provides robust statistical and visual analysis for differential amino acid usage.
  • Case studies demonstrate dagLogo's superior ability to identify and visualize conserved protein patterns.

Conclusions:

  • dagLogo effectively identifies and visualizes conserved protein sequence patterns, including those potentially missed by other methods.
  • The tool provides statistical and visual solutions for analyzing differential amino acid usage in both large and small datasets.
  • dagLogo enhances motif discovery by leveraging reduced amino acid alphabets and offering flexible analysis options.