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

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

11.2K
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...
11.2K
Conservation of Protein Domains02:26

Conservation of Protein Domains

3.2K
3.2K
Protein Networks02:26

Protein Networks

4.1K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
4.1K
Protein-protein Interfaces02:04

Protein-protein Interfaces

12.8K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.8K
Protein and Protein Structures02:15

Protein and Protein Structures

10.7K
10.7K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

11.4K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
11.4K

You might also read

Related Articles

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

Sort by
Same author

Systemic Acquired Resistance signaling molecule N-hydroxypipecolic acid is involved in Age-Related Resistance in Arabidopsis thaliana.

Plant physiology·2026
Same author

Ankh-Score Produces Better Sequence Alignments Than AlphaFold3.

Proteins·2026
Same author

Protein embeddings and local alignments.

Computational and structural biotechnology journal·2026
Same author

Component puzzle protein-protein interaction prediction.

Briefings in bioinformatics·2025
Same author

Explainability of Protein Deep Learning Models.

International journal of molecular sciences·2025
Same author

Reply to: Insufficient evidence for natural selection associated with the Black Death.

Nature·2025
Same journal

GMSA: A Graph Matching and Point Cloud Registration-Based Method for Spatial Transcriptomics Data Alignment.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Investigations on Multiple Protein Scaffold Filling.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Cell Type Prediction for Single-Cell RNA Sequencing Utilizing Unsupervised Domain Adaptation and Semi-Supervised Learning.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

PPIGAN: Prediction of Protein-Protein Interactions Using Generative Adversarial Networks.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Deep Structure-Enhanced Cell Clustering Model for Single-Cell RNA Sequencing Data.

Journal of computational biology : a journal of computational molecular cell biology·2026
Same journal

Asymmetric Drug-Drug Interaction Prediction Based on Generative Adversarial Networks and Knowledge Graph.

Journal of computational biology : a journal of computational molecular cell biology·2026
See all related articles

Related Experiment Video

Updated: Sep 2, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K

Computing Maximal Covers for Protein Sequences.

G Brian Golding1, Holly Koponen2, Neerja Mhaskar2

  • 1Department of Biology, and McMaster University, Hamilton, Ontario, Canada.

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
|August 8, 2022
PubMed
Summary
This summary is machine-generated.

MAXCOVER software efficiently computes maximal covers, which are repeating substrings that cover the most positions in a sequence. This tool is significantly faster and more accurate than existing methods for analyzing protein sequences.

Keywords:
MAXCOVERMUMmerproteinrepeatsstring covers

More Related Videos

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Related Experiment Videos

Last Updated: Sep 2, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

Published on: July 25, 2013

17.1K
Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
07:08

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues

Published on: July 14, 2015

7.4K
A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

68.8K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Defining and identifying repeating substrings within sequences is crucial for biological analysis.
  • Existing methods for finding maximal repeats and covers can be computationally intensive and less precise.

Purpose of the Study:

  • To introduce MAXCOVER, a novel software for the efficient computation of maximal covers (u*) in biological sequences.
  • To compare MAXCOVER's performance against existing software (MUMmer's repeat-match) for identifying maximal repeats.

Main Methods:

  • Utilized data structures developed by Mhaskar and Smyth for efficient computation of maximal covers.
  • Applied the MAXCOVER software to protein sequences from model organisms (Arabidopsis, C. elegans, D. melanogaster) and humans.
  • Extended MAXCOVER and compared its repeat-matching capabilities with MUMmer.

Main Results:

  • MAXCOVER enables the first efficient computation of maximal covers (u*) for any given sequence.
  • MAXCOVER demonstrated an order-of-magnitude speed improvement over MUMmer for repeat analysis.
  • MAXCOVER requires significantly less memory and produces more compact, user-friendly output.

Conclusions:

  • MAXCOVER provides a highly efficient and accurate solution for identifying maximal covers and repeats in biological sequences.
  • The software offers practical advantages in speed, memory usage, and output clarity for bioinformatics research.