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

RNA-seq03:21

RNA-seq

10.0K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
10.0K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

10.9K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.9K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.9K
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...
9.9K

You might also read

Related Articles

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

Sort by
Same author

BAV-LLPS: a database of bacterial, archaea, and virus liquid-liquid phase separation proteins.

Bioinformatics (Oxford, England)·2025
Same author

A STRP-ed definition of Structured Tandem Repeats in Proteins.

Journal of structural biology·2023
Same author

CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure.

Bioinformatics (Oxford, England)·2022
Same author

CoDNaS-RNA: a database of conformational diversity in the native state of RNA.

Bioinformatics (Oxford, England)·2021
Same author

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures.

Nucleic acids research·2020
Same author

Revenant: a database of resurrected proteins.

Database : the journal of biological databases and curation·2020

Related Experiment Video

Updated: Jul 14, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.4K

Daisy: An integrated repeat protein curation service.

Manuel Bezerra-Brandao1, Ronaldo Romario Tunque Cahui1, Layla Hirsh1

  • 1Department of Engineering, Pontifical Catholic University of Peru, Lima 32, Peru.

Journal of Structural Biology
|October 5, 2023
PubMed
Summary

Daisy is a new web service that simplifies the identification and classification of tandem repeats in proteins. It integrates databases and algorithms to accelerate research on repeat proteins.

More Related Videos

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
13:49

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

11.5K
In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
00:06

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

13.7K

Related Experiment Videos

Last Updated: Jul 14, 2025

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

3.4K
Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates
13:49

Semi-automated Biopanning of Bacterial Display Libraries for Peptide Affinity Reagent Discovery and Analysis of Resulting Isolates

Published on: December 6, 2017

11.5K
In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila
00:06

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

13.7K

Area of Science:

  • Bioinformatics
  • Structural Biology
  • Computational Biology

Background:

  • Identifying and classifying tandem repeats in proteins is a challenging manual process.
  • Machine learning advances aid protein structure prediction and repeat classification.
  • Existing services lack integrated databases and software for repeat protein research.

Purpose of the Study:

  • To present Daisy, an integrated web service for curating repeat proteins.
  • To streamline the identification and classification of tandem repeats in protein structures.

Main Methods:

  • Daisy processes Protein Data Bank (PDB) and AlphaFold Database entries.
  • It employs a hidden Markov model (HMM) search against Pfam.
  • Classifications are linked via RepeatsDB and enhance the ReUPred algorithm.

Main Results:

  • Daisy enables efficient tandem repeat identification from PDB and AlphaFold structures.
  • It integrates repeat classifications with identified protein families.
  • The service links protein structures to UniProt proteome data.

Conclusions:

  • Daisy offers a comprehensive solution for repeat protein curation.
  • The web service accelerates the identification and classification of repeat units.
  • It provides valuable resources for researchers studying repeat proteins.