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

Linear Approximation in Frequency Domain01:26

Linear Approximation in Frequency Domain

316
Linear systems are characterized by two main properties: superposition and homogeneity. Superposition allows the response to multiple inputs to be the sum of the responses to each individual input. Homogeneity ensures that scaling an input by a scalar results in the response being scaled by the same scalar.
In contrast, nonlinear systems do not inherently possess these properties. However, for small deviations around an operating point, a nonlinear system can often be approximated as linear....
316
Kendall's Coefficient of Concordance01:20

Kendall's Coefficient of Concordance

890
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...
890
Linear Approximation in Time Domain01:21

Linear Approximation in Time Domain

295
Nonlinear systems often require sophisticated approaches for accurate modeling and analysis, with state-space representation being particularly effective. This method is especially useful for systems where variables and parameters vary with time or operating conditions, such as in a simple pendulum or a translational mechanical system with nonlinear springs.
For a simple pendulum with a mass evenly distributed along its length and the center of mass located at half the pendulum's length,...
295
Extraction: Partition and Distribution Coefficients01:14

Extraction: Partition and Distribution Coefficients

4.5K
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...
4.5K
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation01:24

One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation

1.1K
This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
1.1K
Improving Translational Accuracy02:07

Improving Translational Accuracy

3.5K
3.5K

You might also read

Related Articles

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

Sort by
Same author

Kaminari: a frugal colored index for approximate <i>k</i>-mer queries.

Bioinformatics advances·2026
Same author

Predicting VNN resistance in European sea bass using machine learning on high dimensional low sample size data.

Frontiers in bioinformatics·2026
Same author

Fast Hashing of Spaced Seeds with DuoHash.

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

USTAR-CR: Efficient and Compact Compression of <i>k</i>-Mer Sets Through Colored de Bruijn Graphs.

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

Kaminari: a resource-frugal index for approximate colored <i>k</i>-mer queries.

bioRxiv : the preprint server for biology·2025
Same author

MISSH: Fast Hashing of Multiple Spaced Seeds.

IEEE/ACM transactions on computational biology and bioinformatics·2024

Related Experiment Video

Updated: Jan 1, 2026

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans
07:19

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

Published on: September 13, 2022

2.6K

Indexing k-mers in linear space for quality value compression.

Yoshihiro Shibuya1,2, Matteo Comin1

  • 1Department of Information Engineering, University of Padua, via Gradenigo 6B, Padua, Italy.

Journal of Bioinformatics and Computational Biology
|December 21, 2019
PubMed
Summary

This study introduces a memory-efficient method for building indexed k-mer dictionaries. This approach enhances the compression of sequencing quality scores in FASTQ files while preserving crucial information for SNP calling.

Keywords:
indexingquality scoreread compression

More Related Videos

Quantifying Intermembrane Distances with Serial Image Dilations
07:45

Quantifying Intermembrane Distances with Serial Image Dilations

Published on: September 28, 2018

6.7K
Author Spotlight: Using Hyperpolarized Xenon-129 MRI to Study Lung Diseases
09:55

Author Spotlight: Using Hyperpolarized Xenon-129 MRI to Study Lung Diseases

Published on: January 5, 2024

1.7K

Related Experiment Videos

Last Updated: Jan 1, 2026

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans
07:19

Compost Microcosms as Microbially Diverse, Natural-like Environments for Microbiome Research in Caenorhabditis elegans

Published on: September 13, 2022

2.6K
Quantifying Intermembrane Distances with Serial Image Dilations
07:45

Quantifying Intermembrane Distances with Serial Image Dilations

Published on: September 28, 2018

6.7K
Author Spotlight: Using Hyperpolarized Xenon-129 MRI to Study Lung Diseases
09:55

Author Spotlight: Using Hyperpolarized Xenon-129 MRI to Study Lung Diseases

Published on: January 5, 2024

1.7K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • K-mer dictionaries are crucial for sequence analysis but are often memory-inefficient.
  • Large storage requirements for k-mer dictionaries hinder efficient bioinformatics tool performance.
  • Indexing is necessary for fast queries but exacerbates memory issues.

Purpose of the Study:

  • To develop a memory-efficient indexed linear reference for k-mer sets.
  • To apply this indexed reference to improve the compression of quality scores in FASTQ files.
  • To enhance the compressibility of quality values while retaining information for single nucleotide polymorphism (SNP) calling.

Main Methods:

  • Construction of an indexed linear reference containing input k-mers.
  • Application of the indexed reference for quality score compression in FASTQ files.
  • Utilizing a dictionary of significant k-mers derived from SNP databases and multiple genomes.

Main Results:

  • Demonstrated the ability to index a dictionary of significant k-mers in linear space.
  • Showcased improved compression of quality values using the indexed k-mer dictionary.
  • Preserved essential information for SNP calling during quality score compression.

Conclusions:

  • The proposed method offers a memory-efficient solution for k-mer indexing.
  • This approach significantly improves the compression of sequencing data quality scores.
  • The technique effectively balances compression efficiency with the preservation of critical genetic information.