Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Sequences

Sequences

Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...

Sanger Sequencing

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...

Arithmetic Sequences

Arithmetic Sequences

An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...

Methods for Studying Drug Absorption: In vitro

Methods for Studying Drug Absorption: In vitro

In vitro experiments are crucial for understanding the transport and absorption of drugs through biological materials. These studies employ varied methods such as the diffusion cell method, the everted sac technique, and the everted ring technique.
The diffusion cell method uses a two-compartment cell, including a donor compartment with the drug solution, which simulates the environment where the drug is applied, and a receptor compartment with a buffer solution, which simulates the environment...

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

You might also read

Related Articles

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

Sort by

Same author

Estimating the <i>k</i>-mer Coverage Frequencies in Genomic Datasets: A Comparative Assessment of the State-of-the-art.

Current genomics·2019

See all related articles

Search research articles

Related Experiment Video

Updated: Feb 3, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

A benchmark study of k-mer counting methods for high-throughput sequencing.

Swati C Manekar¹, Shailesh R Sathe¹

¹Department of Computer Science and Engineering, Visvesvaraya National Institute of Technology, Nagpur 440 010, India.

|October 23, 2018

Summary

This study evaluates k-mer counting tools for large sequencing datasets, comparing performance based on speed and memory. Recommendations are provided for optimal bioinformatics tool setup and future development.

More Related Videos

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Related Experiment Videos

Last Updated: Feb 3, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

A Protocol for Functional Assessment of Whole-Protein Saturation Mutagenesis Libraries Utilizing High-Throughput Sequencing

Published on: July 3, 2016

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

Published on: May 23, 2018

Area of Science:

Bioinformatics
Computational Biology
Genomics

Background:

High-throughput sequencing generates massive datasets (hundreds of gigabytes).
Bioinformatics tools often require counting k-mers (substrings of length k) in DNA/RNA sequencing reads.
Applications include genome assembly, error correction, and repeat detection.

Purpose of the Study:

To assess and compare the performance of various k-mer counting programs.
To evaluate trade-offs between time and memory usage for k-mer counting.
To provide recommendations for current state-of-the-art k-mer counting tool setup.

Main Methods:

Evaluated multiple k-mer counting programs.
Measured performance based on runtime and memory usage.
Assessed additional parameters: disk usage, accuracy, parallelism, compressed input, large k-value performance, and scalability.

Main Results:

Identified performance trade-offs among different k-mer counting techniques.
Detailed analysis of runtime, memory, and other key performance indicators.
Comparative evaluation of tools for handling large sequencing datasets.

Conclusions:

Specific recommendations for setting up optimal k-mer counting tools.
Suggestions for future development directions in k-mer counting software.
Guidance for researchers selecting k-mer counting methods for large-scale sequencing projects.