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

RNA-seq03:21

RNA-seq

12.1K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
12.1K
Comparing the Survival Analysis of Two or More Groups01:20

Comparing the Survival Analysis of Two or More Groups

597
Survival analysis is a cornerstone of medical research, used to evaluate the time until an event of interest occurs, such as death, disease recurrence, or recovery. Unlike standard statistical methods, survival analysis is particularly adept at handling censored data—instances where the event has not occurred for some participants by the end of the study or remains unobserved. To address these unique challenges, specialized techniques like the Kaplan-Meier estimator, log-rank test, and...
597
Inertial Frames of Reference01:03

Inertial Frames of Reference

8.8K
Newton’s first law is usually considered to be a statement about reference frames. It provides a method for identifying a special type of reference frame: the inertial reference frame. In principle, we can make the net force on a body zero. If its velocity relative to a given frame is constant, then that frame is said to be inertial. So, by definition, an inertial reference frame is a reference frame where Newton's first law holds valid. Newton's first law applies to objects with...
8.8K
Non-inertial Frames of Reference01:27

Non-inertial Frames of Reference

7.2K
A reference frame accelerating or decelerating relative to an inertial frame is a non-inertial frame. To help understand this, consider what taking off in an airplane, turning a corner in a car, riding a merry-go-round, and the circular motion of a tropical cyclone all have in common. All these systems are accelerating, decelerating, or rotating relative to the Earth; hence, they all are non-inertial frames. All these systems exhibit inertial forces, which merely seem to arise from motion,...
7.2K
Directing Effect of Substituents: meta-Directing Groups01:09

Directing Effect of Substituents: meta-Directing Groups

6.0K
Substituents on the benzene ring that direct an incoming electrophile to undergo substitution at the meta position are called meta directors. All meta directors either have a positive charge on the atom directly bonded to the ring or a partial positive charge. These groups function by withdrawing electrons from the ring through inductive and resonance effects. Consider the carbocation intermediates formed upon the addition of an electrophile on nitrobenzene at the...
6.0K
RNA Stability01:53

RNA Stability

35.7K
Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
35.7K

You might also read

Related Articles

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

Sort by
Same author

Segregating BC<sub>2</sub>F<sub>1</sub> interspecific hybrids between <i>Brassica napus</i> and <i>B. nigra</i> reveal a major effect locus for blackleg resistance on chromosome B2.

Molecular breeding : new strategies in plant improvement·2026
Same author

Genomic advances in orphan and underutilized Brassicaceae crops and their wild relatives.

Frontiers in plant science·2026
Same author

Identification of a QTL conferring resistance to the Subtropical Race 4 of <i>Fusarium oxysporum</i> f. sp. <i>cubense</i> in Calcutta 4 (<i>Musa acuminata</i> ssp. <i>burmannica</i>).

Horticulture research·2026
Same author

Dissection of local haplotype diversity at soybean rust loci reveals resistance-associated and context-dependent variation patterns in diverse germplasm.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2026
Same author

Temporal stability and spatial patterns of genetic diversity in populations of the climate-vulnerable fucoid Scytothalia dorycarpa.

Journal of phycology·2026
Same author

Accessing crop genetic diversity via pangenomics.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2026

Related Experiment Video

Updated: Feb 2, 2026

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

22.4K

A differential k-mer analysis pipeline for comparing RNA-Seq transcriptome and meta-transcriptome datasets without a

Chon-Kit Kenneth Chan1,2, Nedeljka Rosic3,4, Michał T Lorenc5

  • 1School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.

Functional & Integrative Genomics
|November 29, 2018
PubMed
Summary
This summary is machine-generated.

A new k-mer based pipeline, DiffKAP, identifies differential gene expression from RNA-Seq data without needing a reference genome. This method accurately analyzes complex meta-transcriptomes, overcoming limitations of traditional approaches.

Keywords:
CoralHost-microbe symbiosisK-mer analysisMeta-transcriptomeRNA-SeqSoybean

More Related Videos

Mining Spatial Transcriptomics Datasets using DeepSpaceDB
10:16

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

769
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

4.8K

Related Experiment Videos

Last Updated: Feb 2, 2026

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells
18:30

RNA-seq Analysis of Transcriptomes in Thrombin-treated and Control Human Pulmonary Microvascular Endothelial Cells

Published on: February 13, 2013

22.4K
Mining Spatial Transcriptomics Datasets using DeepSpaceDB
10:16

Mining Spatial Transcriptomics Datasets using DeepSpaceDB

Published on: September 5, 2025

769
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
14:58

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

4.8K

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA-Sequencing (RNA-Seq) is crucial for genome-wide gene expression studies.
  • Traditional analysis relies on mapping reads to a reference genome, which is often unavailable for meta-transcriptomics.
  • De novo assembly is challenging and costly, especially for mixed organism datasets.

Purpose of the Study:

  • To develop a reference-free method for differential gene expression analysis of RNA-Seq data.
  • To provide an accurate alternative for complex meta-transcriptome studies lacking reference genomes.

Main Methods:

  • Developed DiffKAP, a k-mer based analysis pipeline for differential read expression.
  • Compared DiffKAP to Tophat/Cuffdiff using soybean RNA-Seq data with a reference genome.
  • Applied DiffKAP to a coral meta-transcriptome dataset and validated with qRT-PCR.

Main Results:

  • DiffKAP demonstrated accuracy comparable to reference-based methods in soybean.
  • Successfully identified differentially expressed genes in a coral meta-transcriptome without a reference.
  • qRT-PCR validation confirmed the accuracy of DiffKAP's findings in the coral study.

Conclusions:

  • DiffKAP is an accurate and effective tool for differential gene expression analysis.
  • The pipeline overcomes the need for a reference genome, broadening RNA-Seq applications in complex biological systems.
  • DiffKAP offers a valuable solution for meta-transcriptome studies.