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

Histone Variants at the Centromere02:30

Histone Variants at the Centromere

5.1K
Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
5.1K
Drug Discovery: Overview01:26

Drug Discovery: Overview

11.6K
Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
11.6K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

11.8K
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...
11.8K
Sequences01:29

Sequences

277
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...
277
Sanger Sequencing01:57

Sanger Sequencing

774.5K
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...
774.5K
Arithmetic Sequences01:30

Arithmetic Sequences

239
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...
239

You might also read

Related Articles

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

Sort by
Same author

Macrophage Plasticity and Immune Remodeling in Ischemic Heart Failure.

Immunological reviews·2026
Same author

Human Fibroblast-Myeloid Cell Tissue Atlas Across the Lungs, Synovium, Skin, and Heart.

Arthritis & rheumatology (Hoboken, N.J.)·2026
Same author

Allelic diversity of the pharmacogenes CYP2D6 and CYP2C19 in Māori from Te Tairāwhiti, Aotearoa New Zealand.

Frontiers in genetics·2026
Same author

The ontogeny of myeloid-stromal synovial tissue niches in rheumatoid arthritis.

Research square·2025
Same author

The ontogeny of myeloid-stromal synovial tissue niches in rheumatoid arthritis.

bioRxiv : the preprint server for biology·2025
Same author

Misclassified latent autoimmune diabetes in adults within Māori and Pacific adults with type 2 diabetes in Aotearoa New Zealand.

The New Zealand medical journal·2025

Related Experiment Video

Updated: Feb 3, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.7K

Approaches to variant discovery for conifer transcriptome sequencing.

Emily Telfer1, Natalie Graham1, Lucy Macdonald1

  • 1New Zealand Forest Research Institute LTD. trading as Scion, Rotorua, New Zealand.

Plos One
|November 6, 2018
PubMed
Summary

Comparing bioinformatic tools for RNA sequencing is crucial for identifying genetic markers in Pinus radiata. Different software combinations significantly impact single nucleotide polymorphism (SNP) discovery, highlighting the need for optimized pipelines in tree breeding.

More Related Videos

Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.1K
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

14.3K

Related Experiment Videos

Last Updated: Feb 3, 2026

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

15.7K
Novel Sequence Discovery by Subtractive Genomics
09:40

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

9.1K
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
09:58

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

Published on: December 9, 2016

14.3K

Area of Science:

  • Bioinformatics
  • Genomics
  • Plant Breeding

Background:

  • Operational breeding programs aim to integrate genomics tools for genetic improvement.
  • Large conifer genomes lack complete reference sequences, necessitating alternative marker discovery methods.
  • RNA sequencing provides a valuable source of genetic markers for species like Pinus radiata.

Purpose of the Study:

  • To compare the performance of different bioinformatic tool combinations for SNP discovery from transcriptomic data.
  • To identify an optimal pipeline for variant calling in Pinus radiata.
  • To assess the utility of RNA sequencing for large-scale genetic marker identification in conifers.

Main Methods:

  • Evaluated nine different assembler and variant calling software combinations using a single transcriptomic library.
  • Applied the best-performing assembler (Trinity) and variant callers to a larger, multi-genotype, multi-tissue transcriptome dataset.
  • Mapped identified SNPs to the Pinus taeda reference genome (ver 1.01e).

Main Results:

  • Single nucleotide polymorphism (SNP) discovery varied significantly, from 8,061 to 86,815 SNPs across tested software combinations.
  • The Trinity assembler showed superior realignment performance.
  • A comprehensive analysis identified 683,135 in silico SNPs within approximately 449,951 exons.

Conclusions:

  • The choice of bioinformatic tools critically influences the number of identified SNPs.
  • RNA sequencing coupled with optimized bioinformatics pipelines is effective for discovering a large number of genetic markers in Pinus radiata.
  • This approach facilitates the integration of genomics into breeding programs for this important tree species.