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

12.3K
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...
12.3K
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

4.9K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.9K
Sanger Sequencing01:57

Sanger Sequencing

776.1K
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...
776.1K
Next-generation Sequencing03:00

Next-generation Sequencing

99.6K
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....
99.6K
Maxam-Gilbert Sequencing01:05

Maxam-Gilbert Sequencing

13.3K
In the same year as the discovery of the Sanger sequencing method, another group of scientists, Allan Maxam and Walter Gilbert, demonstrated their chemical-cleavage method for DNA sequencing. The Maxam-Gilbert method relies on using different chemicals that can cleave the DNA sequence at specific sites, the separation of resulting DNA fragments of variable size using electrophoresis, and deciphering the DNA sequence from the resulting gel bands.
Challenges of the Maxam-Gilbert Method
The...
13.3K
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

12.0K
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...
12.0K

You might also read

Related Articles

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

Sort by
Same author

Genetic loss of CHD1 regulates distinct histone post-translational modifications in the development of castration-resistant prostate cancer.

Neoplasia (New York, N.Y.)·2026
Same author

cfOncoXpress: Tumor gene expression prediction from cell-free DNA whole-genome sequences.

bioRxiv : the preprint server for biology·2025
Same author

Disinfection of Hospital Sink Drains Enriches Pseudomonadota and Efflux Pump-Mediated Antibiotic Resistance in Reestablished Biofilms.

Research square·2025
Same author

Network-based drug repurposing for psychiatric disorders using single-cell genomics.

Cell genomics·2025
Same author

Risks of AI scientists: prioritizing safeguarding over autonomy.

Nature communications·2025
Same author

Regulatory genome annotation.

Nature reviews. Genetics·2025
Same journal

Protein Sequence Analysis Using the MPI Bioinformatics Toolkit.

Current protocols in bioinformatics·2020
Same journal

Exploring Manually Curated Annotations of Intrinsically Disordered Proteins with DisProt.

Current protocols in bioinformatics·2020
Same journal

Network Building with the Cytoscape BioGateway App Explained in Five Use Cases.

Current protocols in bioinformatics·2020
Same journal

Expanding the Perseus Software for Omics Data Analysis With Custom Plugins.

Current protocols in bioinformatics·2020
Same journal

Exploring Non-Coding RNAs in RNAcentral.

Current protocols in bioinformatics·2020
Same journal

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource.

Current protocols in bioinformatics·2020
See all related articles

Related Experiment Video

Updated: Mar 3, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

11.0K

Using FunSeq2 for Coding and Non-Coding Variant Annotation and Prioritization.

Priyanka Dhingra1,2, Yao Fu3, Mark Gerstein4,5,6

  • 1Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York.

Current Protocols in Bioinformatics
|May 3, 2017
PubMed
Summary
This summary is machine-generated.

Identifying non-coding mutations is difficult for clinical whole-genome sequencing. FunSeq2 is a computational tool that annotates and prioritizes somatic mutations in both coding and non-coding regions.

Keywords:
cancer driversdifferential gene expressiondisease-causingindelsnon-coding variantssingle nucleotide variants

More Related Videos

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
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.9K

Related Experiment Videos

Last Updated: Mar 3, 2026

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

11.0K
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
Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
07:30

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

12.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying non-coding mutations poses a significant challenge for clinical applications of whole-genome sequencing.
  • Non-coding variants are often overlooked, yet can play crucial roles in disease development.

Purpose of the Study:

  • To introduce FunSeq2, a computational tool designed for the annotation and prioritization of somatic mutations.
  • To provide guidelines for installing and utilizing FunSeq2 for variant analysis and gene expression detection.

Main Methods:

  • FunSeq2 integrates a comprehensive data context from large-scale genomic datasets.
  • It employs a high-throughput variant prioritization pipeline for efficient analysis.
  • The tool supports annotation and prioritization of variants in both coding and non-coding regions.

Main Results:

  • FunSeq2 enables the annotation and prioritization of somatic mutations.
  • The tool allows for the incorporation of user-defined annotations.
  • FunSeq2 can be used to detect differential gene expression.

Conclusions:

  • FunSeq2 offers a valuable computational solution for analyzing both coding and non-coding mutations.
  • The tool facilitates the clinical utility of whole-genome sequencing by addressing the challenge of variant identification.
  • Guidelines are provided for practical implementation and application of FunSeq2.