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

12.2K
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...
12.2K
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

18.8K
Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
18.8K

You might also read

Related Articles

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

Sort by
Same author

Direct extraction of bromine from seawater through an electrolysis-driven styrene enrichment process.

Nature communications·2026
Same author

PAPS1-associated alternative polyadenylation changes correlate with pollen development and flowering time in Arabidopsis.

Plant physiology·2026
Same author

Effects of probiotic fermentation on Gracilaria bailinae polysaccharides: Characterization and immunomodulatory potency.

International journal of biological macromolecules·2026
Same author

Programmable mRNA 3'UTR engineering restores MHC-I and overcomes immune evasion in prostate cancer.

Nature biomedical engineering·2026
Same author

Microbial and enzymatic degradation of plastics: Opportunities and constraints for plastic waste remediation.

Biotechnology advances·2026
Same author

Tailoring Preservation to Form: A Comparative Review of Postharvest Technologies for Three Types of Fresh Walnuts.

Journal of food science·2026
Same journal

CNV-ECOD: A copy number variation detection method based on ECOD algorithm using next-generation sequencing data.

Journal of bioinformatics and computational biology·2026
Same journal

ReinVar: A model-free paradigm-based reinforcement learning approach to detect copy number variation.

Journal of bioinformatics and computational biology·2026
Same journal

When pipelines run but coordinates fail: A simple spatial specificity check for false locality in post-GWAS analysis.

Journal of bioinformatics and computational biology·2026
Same journal

Comparative benchmarking of template-based, evolutionary-diffusion, and generative language models for IsPETase structure prediction.

Journal of bioinformatics and computational biology·2026
Same journal

Trap spaces as labelled ideals of SCC posets: A structural-functional theory of reachability in asynchronous boolean networks.

Journal of bioinformatics and computational biology·2026
Same journal

Erratum - DDINet: Drug-drug interaction prediction network based on multi-molecular fingerprint features and multi-head attention centered weighted autoencoder.

Journal of bioinformatics and computational biology·2026
See all related articles

Related Experiment Video

Updated: Feb 23, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.5K

PAcluster: Clustering polyadenylation site data using canonical correlation analysis.

Guoli Ji1, Qianmin Lin1, Yuqi Long1

  • 1* Department of Automation, Xiamen University, Xiamen, Fujian, P. R. China.

Journal of Bioinformatics and Computational Biology
|September 7, 2017
PubMed
Summary
This summary is machine-generated.

This study introduces a novel computational method for clustering alternative polyadenylation (APA) sites, improving the identification of co-regulated genes. The PAcluster R package offers an efficient solution for analyzing large APA datasets.

Keywords:
Polyadenylationalternative polyadenylationcanonical correlation analysiscluster analysissoftware

More Related Videos

3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

11.1K
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

4.3K

Related Experiment Videos

Last Updated: Feb 23, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

6.5K
3' End Sequencing Library Preparation with A-seq2
12:01

3' End Sequencing Library Preparation with A-seq2

Published on: October 10, 2017

11.1K
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

4.3K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Alternative polyadenylation (APA) is a key gene regulatory mechanism.
  • Advancements in sequencing necessitate improved computational tools for APA analysis.
  • Existing clustering methods often overlook crucial APA site characteristics like distribution and abundance.

Purpose of the Study:

  • To develop a novel computational method for clustering poly(A) sites to better understand APA regulation.
  • To address limitations in current clustering approaches for APA data.
  • To identify genes with correlated APA patterns for biologically meaningful clustering.

Main Methods:

  • Constructed a two-layer model utilizing canonical correlation analysis (CCA).
  • The first layer quantifies general APA site correlation across conditions for each gene.
  • The second layer identifies genes with statistically significant APA pattern correlations.

Main Results:

  • The CCA-based method significantly improved clustering performance on both synthetic and real poly(A) site data.
  • Generated clusters with enhanced biological relevance compared to existing methods.
  • Demonstrated superior performance against four other widely used distance measures.

Conclusions:

  • The developed CCA-based method provides a robust approach for APA site clustering.
  • The PAcluster R package offers an efficient tool for analyzing large-scale APA data.
  • This method facilitates deeper insights into the biological mechanisms of APA regulation.