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

Structure of Benzene: Kekulé Model01:07

Structure of Benzene: Kekulé Model

10.8K
In 1865, August Kekule suggested the structure of benzene according to the structural theory of organic chemistry based on the three assertions—formula of benzene is C6H6, all the hydrogens of benzene are equivalent, and each carbon must have four bonds due to its tetravalency.
He proposed that benzene has a cyclic structure of six carbon atoms attached to one hydrogen atom each, with three alternating pi bonds.
10.8K
Structures of Aldehydes and Ketones01:04

Structures of Aldehydes and Ketones

10.9K
Vanillin—a flavoring agent in vanilla, cinnamaldehyde—a molecule responsible for the distinct smell of cinnamon, and acetone—a strong-smelling ingredient in nail polish removers, all belong to a class of carbonyl compounds called aldehydes and ketones (Figure 1). Although both aldehydes and ketones contain the characteristic carbonyl (C=O) bond, their chemical structures vary with respect to the groups directly attached to the carbonyl carbon.
In aldehydes (Figures 1a and 1b), the...
10.9K
Resonance and Hybrid Structures02:16

Resonance and Hybrid Structures

22.6K
According to the theory of resonance, if two or more Lewis structures with the same arrangement of atoms can be written for a molecule, ion, or radical, the actual distribution of electrons is an average of that shown by the various Lewis structures.
Resonance Structures and Resonance Hybrids
The Lewis structure of a nitrite anion (NO2−) may actually be drawn in two different ways, distinguished by the locations of the N–O and N=O bonds.
22.6K
Nucleic Acid Structure01:25

Nucleic Acid Structure

7.8K
The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA...
7.8K
Structure of Alkanes02:23

Structure of Alkanes

31.1K
The formation of carbon-carbon bonds leading to the creation of the carbon chain is the basis of organic chemistry. August Kekulé and Archibald Scott Couper independently developed this idea of carbon chain formation.
Hydrocarbons are the simplest organic compounds composed of carbons and hydrogens. Based on the bond order between carbons, the hydrocarbons are further classified into alkanes, alkenes, and alkynes. 
Alkanes are the simplest hydrocarbons with sp3 hybrid carbon atoms....
31.1K
Isomerism in Alkenes02:01

Isomerism in Alkenes

13.7K
Alkenes like 1-butene and 2-butene exhibit constitutional isomerism, as they differ in the position of the double bond. Further, 2-butene exhibits stereoisomerism and exists as two distinct compounds differing in spatial arrangement.
An isomer is called cis-2-butene when the methyl groups are on the same side of the double bond, and the other stereoisomer, in which methyl groups are on the opposite side of the double bond, is called trans-2-butene. The cis and trans stereoisomers are not...
13.7K

You might also read

Related Articles

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

Sort by
Same author

Metappuccino: large language model-driven reconstruction of sequence read archive metadata for cancer research.

Bioinformatics (Oxford, England)·2026
Same author

Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors.

PeerJ·2026
Same author

K2R: Tinted de Bruijn graphs implementation for efficient read extraction from sequencing datasets.

Bioinformatics advances·2025
Same author

OReO: optimizing read order for practical compression.

Bioinformatics advances·2025
Same author

Fractional hitting sets for efficient multiset sketching.

Algorithms for molecular biology : AMB·2025
Same author

Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets.

Bioinformatics (Oxford, England)·2024
Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026
Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026
Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026
Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026
Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026
Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026
See all related articles

Related Experiment Video

Updated: Nov 10, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

2.8K

BLight: efficient exact associative structure for k-mers.

Camille Marchet1, Mael Kerbiriou1, Antoine Limasset1

  • 1University of Lille, CRIStAL CNRS, UMR 9189 - F-59000 Lille, France.

Bioinformatics (Oxford, England)
|April 6, 2021
PubMed
Summary
This summary is machine-generated.

BLight is a new data structure that efficiently indexes billions of k-mers for high-throughput sequencing analysis. It offers low memory usage and fast query speeds, making large-scale genomics accessible.

More Related Videos

A Guide to Production, Crystallization, and Structure Determination of Human IKK1/α
11:27

A Guide to Production, Crystallization, and Structure Determination of Human IKK1/α

Published on: November 2, 2018

9.3K
Identification of Functional Protein Regions Through Chimeric Protein Construction
11:39

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

10.7K

Related Experiment Videos

Last Updated: Nov 10, 2025

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids
08:21

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Published on: April 13, 2022

2.8K
A Guide to Production, Crystallization, and Structure Determination of Human IKK1/α
11:27

A Guide to Production, Crystallization, and Structure Determination of Human IKK1/α

Published on: November 2, 2018

9.3K
Identification of Functional Protein Regions Through Chimeric Protein Construction
11:39

Identification of Functional Protein Regions Through Chimeric Protein Construction

Published on: January 8, 2019

10.7K

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput sequence analysis requires associating information with k-mers.
  • Indexing billions of k-mers presents scalability and memory challenges with existing methods.
  • Current data structures are often unable to associate information or are not memory-efficient.

Purpose of the Study:

  • To present BLight, a static and exact data structure for k-mer indexing.
  • To enable association of unique identifiers to k-mers and set membership determination.
  • To provide a scalable, low-memory, and fast solution for large k-mer sets.

Main Methods:

  • Developed BLight as a static and exact data structure.
  • Implemented BLight in C++ as an open-source library.
  • Evaluated BLight's performance on human and axolotl genomes.

Main Results:

  • BLight achieves low memory cost (23-27 bits per k-mer) and efficient construction.
  • Indexing human genome k-mers took 10 min with 8 GB RAM; axolotl genome took 76 min with 63 GB RAM.
  • Demonstrated high query throughput: 1.4 million/sec (single CPU) to 16.1 million/sec (12 cores).
  • Showcased BLight's applicability to metagenomic and transcriptomic data.

Conclusions:

  • BLight offers a scalable, memory-efficient, and fast solution for k-mer indexing.
  • The data structure is suitable for large-scale genomic, metagenomic, and transcriptomic analyses.
  • BLight is available as an open-source C++ library with usage samples.