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

RNA-seq

RNA-seq

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...

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....

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...

You might also read

Related Articles

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

Sort by

Same author

ddRAD sequencing of 1076 <i>Camellia</i> accessions reveals the genetic diversity and population introgression of the tea plant in China.

Plant diversity·2026

Same author

Mitochondrial uncoupling protein SpUCP regulates redox homeostasis and enhances heavy metal tolerance in mud crab (Scylla paramamosain) exposed to copper and cadmium.

Marine environmental research·2026

Same author

Perlucin, a novel C-type lectin from the mud crab Scylla paramamosain, modulates innate immunity and enhances tolerance to Vibrio parahaemolyticus infection and ammonia stress.

Comparative biochemistry and physiology. Toxicology & pharmacology : CBP·2026

Same author

Characterization of Rice Volatile Secondary Metabolites and Their Role in Modulating the Behavior of the Brown Planthopper (<i>Nilaparvata lugens</i> Stål).

Insects·2026

Same author

DJ-1 regulates innate immune defense and antioxidant response against Vibrio parahaemolyticus infection in the mud crab Scylla paramamosain.

Fish & shellfish immunology·2026

Same author

Physiological and transcriptomic insights into the stress response of mud crab Scylla paramamosain (Estampador, 1950) to low salinity.

Marine environmental research·2026

Search research articles

Related Experiment Video

Updated: Mar 27, 2026

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled

En-Hua Xia¹, Qiu-Yang Yao¹, Hai-Bin Zhang¹

¹Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China; University of Chinese Academy of SciencesBeijing, China.

Frontiers in Plant Science

|January 19, 2016

Summary

CandiSSR is a new pipeline for identifying simple sequence repeats (SSRs) or microsatellites. This tool efficiently finds polymorphic SSRs (PolySSRs) in genomes and transcriptomes, aiding genetic analysis and breeding programs.

Keywords:

CandiSSR microsatellites multiple assembled genomes multiple assembled transcriptomes polymorphic SSR transferability

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Related Experiment Videos

Last Updated: Mar 27, 2026

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Single Cell Multiplex Reverse Transcription Polymerase Chain Reaction After Patch-clamp

Published on: June 20, 2018

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Simple sequence repeats (SSRs), or microsatellites, are valuable molecular markers for genetic analysis due to their high mutation rates.
Traditional SSR screening is labor-intensive and time-consuming, limiting large-scale applications.
Advancements in next-generation sequencing provide opportunities for efficient SSR discovery.

Purpose of the Study:

To develop a novel bioinformatics pipeline, CandiSSR, for large-scale identification of candidate polymorphic SSRs (PolySSRs).
To enable PolySSR discovery from both assembled genome and transcriptome datasets.
To provide confidence metrics and primer design for SSR marker development.

Main Methods:

Developed CandiSSR pipeline for identifying PolySSRs from multiple assembled sequences.
Incorporated standard deviation and missing rate metrics for assessing SSR feasibility.
Automated primer pair design and evaluation based on sequence similarity.
Validated CandiSSR using rice genomes, achieving over 90% accuracy.

Main Results:

CandiSSR successfully identified candidate PolySSRs from rice, Arabidopsis, and Camellia datasets.
The pipeline demonstrated high accuracy (>90%) in experimental validation.
Automated primer design and evaluation enhance marker development success rates.
Provided confidence metrics for systematic assessment of PolySSRs.

Conclusions:

CandiSSR offers an efficient and accurate solution for identifying polymorphic SSRs from diverse sequence data.
The pipeline facilitates large-scale SSR marker discovery for genetic studies and breeding.
CandiSSR enhances the application of SSRs in genomics and molecular breeding programs.