Related Experiment Video
Updated: Sep 2, 2025
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.
Summary
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.
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.
More Related Videos
Related Concept Videos
02:26Conservation 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...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.2K
02:26Conservation of Protein Domains
3.2K
3.2K
02:26Protein 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,...
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
02:04Protein-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
02:15Protein and Protein Structures
10.7K
10.7K
01:05Maxam-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...
Challenges of the Maxam-Gilbert Method
The...
11.4K