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

Compacting Factor test01:22

Compacting Factor test

334
The compacting factor test is a method used to assess the workability of concrete. It is  especially suitable for concrete mixes containing aggregates up to one and a half inches in size. This test involves specialized equipment consisting of two truncated cone-shaped hoppers and a cylinder, all with polished interior surfaces to minimize friction.
The procedure begins by placing concrete into the upper hopper without any compaction. Once filled, the bottom door of this hopper is opened,...
334
Extraction: Partition and Distribution Coefficients01:14

Extraction: Partition and Distribution Coefficients

3.8K
The distribution law or Nernst's distribution law is the law that governs the distribution of a solute between two immiscible solvents. This law, also known as the partition law, states that if a solute is added to the mixture of two immiscible solvents at a constant temperature, the solute is distributed between the two solvents in such a way that the ratio of solute concentrations in the solvents remains constant at equilibrium.
For extracting a solute from an aqueous phase into an...
3.8K
Kendall's Coefficient of Concordance01:20

Kendall's Coefficient of Concordance

654
Kendall's Coefficient of Concordance (W), also known as Kendall's W, is a non-parametric statistical measure used to assess the agreement or concordance between multiple raters or judges when they rank a set of items. It is often used when you have ordinal data (ranks) and you want to see if there is consistency or consensus among the raters. It is widely applied in research areas such as psychology, medicine, and social sciences, where multiple judges are asked to rank or rate subjects...
654
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.4K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.4K
Downsampling01:20

Downsampling

337
When considering a sampled sequence with zero values between sampling instants, one can replace it by taking every N-th value of the sequence. At these integer multiples of N, the original and sampled sequences coincide. This process, known as decimation, involves extracting every N-th sample from a sequence, thereby creating a more efficient sequence.
The Fourier transform of the decimated sequence reveals a combination of scaled and shifted versions of the original spectrum. This...
337
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.5K
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...
13.5K

You might also read

Related Articles

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

Sort by
Same authorSame journal

A k-mer-based estimator of the substitution rate between repetitive sequences.

Algorithms for molecular biology : AMB·2026
Same author

EGGS: Empirical Genotype Generalizer for Samples.

Bioinformatics advances·2026
Same author

A versatile multi-components mixed model for bacterial-Genome Wide association studies.

Nature communications·2026
Same author

Hash functions in nucleotide sequence analysis.

Genome research·2026
Same author

Estimation of substitution and indel rates via <i>k</i>-mer statistics.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2026
Same author

A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences.

Algorithms in bioinformatics : ... International Workshop, WABI ..., proceedings. WABI (Workshop)·2026
Same journal

Haplotype-aware long-read error correction.

Algorithms for molecular biology : AMB·2026
Same journal

Extension of partial atom-to-atom maps: uniqueness and algorithms.

Algorithms for molecular biology : AMB·2026
Same journal

Lossless pangenome indexing using tag arrays.

Algorithms for molecular biology : AMB·2026
Same journal

Dolphyin: a combinatorial algorithm for identifying 1-Dollo phylogenies in cancer.

Algorithms for molecular biology : AMB·2026
Same journal

Probing transcription factor subsets in gene regulatory networks.

Algorithms for molecular biology : AMB·2026
See all related articles

Related Experiment Video

Updated: Nov 1, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

346

Disk compression of k-mer sets.

Amatur Rahman1, Rayan Chikhi2, Paul Medvedev3

  • 1Penn State University, State College, PA, USA. aur1111@psu.edu.

Algorithms for Molecular Biology : AMB
|June 22, 2021
PubMed
Summary
This summary is machine-generated.

New compression methods, ESS-Compress and ESS-Tip-Compress, significantly reduce the storage size of k-mer datasets. These bioinformatics tools improve upon UST-Compress by up to 27%, aiding large dataset management and reproducibility.

Keywords:
CompressionDe Bruijn graphsSpectrum-preserving string setsk-mer sets

More Related Videos

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.3K
Quantifying Intermembrane Distances with Serial Image Dilations
07:45

Quantifying Intermembrane Distances with Serial Image Dilations

Published on: September 28, 2018

6.6K

Related Experiment Videos

Last Updated: Nov 1, 2025

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles
10:23

A Concoction Pipeline for Generating Molecular Operational Taxonomic Units (MOTUs) Among Riparian and Aquatic Beetles

Published on: July 11, 2025

346
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.3K
Quantifying Intermembrane Distances with Serial Image Dilations
07:45

Quantifying Intermembrane Distances with Serial Image Dilations

Published on: September 28, 2018

6.6K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Data Compression

Background:

  • K-mer based methods are crucial in bioinformatics, often processing massive multi-terabyte datasets.
  • Current compression methods are suboptimal for k-mer sets due to unaddressed redundancy patterns.
  • Efficient storage is vital for tool developers, users, and ensuring research reproducibility.

Purpose of the Study:

  • To introduce and evaluate two novel disk compression algorithms for k-mer sets: ESS-Compress and ESS-Tip-Compress.
  • To improve upon the existing UST-Compress algorithm by further reducing data redundancy.
  • To analyze the theoretical and practical performance of the new compression strategies.

Main Methods:

  • Development of ESS-Compress and ESS-Tip-Compress algorithms based on a relaxed string set representation.
  • Theoretical analysis of the compression strategies.
  • Empirical evaluation using diverse real-world datasets.

Main Results:

  • ESS-Compress and ESS-Tip-Compress achieve improved compression ratios compared to UST-Compress.
  • Compression size reductions of up to 27% were observed across various datasets.
  • Theoretical lower bounds for this compression strategy were derived.

Conclusions:

  • ESS-Compress and ESS-Tip-Compress offer significant advancements in compressing large k-mer datasets.
  • These methods enhance storage efficiency and support reproducibility in bioinformatics.
  • The study provides a theoretical foundation for future k-mer compression research.