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

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Genome-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

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...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

You might also read

Related Articles

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

Sort by

Same author

A lethal form of ASCC3 disease: severe global developmental delay, axial hypotonia, hypoplasia of corpus callosum, hypothyroidism and micropenis.

HGG advances·2026

Same author

FACS-based dual fluorescence reporter assay demonstrates efficacy of antisense oligonucleotide therapy of novel <i>PRPF3</i> intronic splice variant.

Molecular therapy. Nucleic acids·2026

Same author

The Genetic Landscape of Inherited Retinal Diseases in the Israeli Population.

Investigative ophthalmology & visual science·2026

Same author

A ciliopathy combining Joubert syndrome and Oro-Facial-Digital syndrome caused by bi-allelic 5'-UTR loss-of-function CEP83 variant.

NPJ genomic medicine·2025

Same author

Intronic and Coding Genetic Variants in Autosomal Recessive Polycystic Kidney Disease Among Israeli Bedouins of Arabian Peninsula Ancestry.

American journal of kidney diseases : the official journal of the National Kidney Foundation·2025

Same author

Early-Onset Movement Disorder Syndrome Caused by Biallelic Variants in PDE1B Encoding Phosphodiesterase 1B.

Movement disorders : official journal of the Movement Disorder Society·2025

Same journal

Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.

Database : the journal of biological databases and curation·2026

Same journal

KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.

Database : the journal of biological databases and curation·2026

Same journal

PhaLP 2.0: extending the community-oriented phage lysin database with a SUBLYME pipeline for metagenomic discovery.

Database : the journal of biological databases and curation·2026

Same journal

A similarity metric, rubric, and unified hierarchy for biomedical publication types and study designs.

Database : the journal of biological databases and curation·2026

Same journal

GUTAID: a curated database linking gut microbial antigens to autoimmune mechanisms.

Database : the journal of biological databases and curation·2026

Same journal

Rosetta Statements: simplifying FAIR knowledge graph construction with a user-centred approach.

Database : the journal of biological databases and curation·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jul 26, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture.

Noam Hadar^1,2, Grisha Weintraub³, Ehud Gudes³

¹The Morris Kahn Laboratory of Human Genetics at the National Institute of Biotechnology in the Negev and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel.

Database : the Journal of Biological Databases and Curation

|June 13, 2023

Summary

This summary is machine-generated.

GeniePool offers easy access to human genomic and phenotypic data from the Sequence Read Archive (SRA). This new web service and API simplifies querying next-generation sequencing (NGS) data for clinical and research applications.

More Related Videos

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Published on: January 13, 2019

Related Experiment Videos

Last Updated: Jul 26, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

Published on: January 13, 2019

Area of Science:

Genomics
Bioinformatics
Data Science

Background:

Growing influx of genomic data necessitates integrated phenotypic correlations.
Existing databases lack easy storage and accessibility for combined genotypic-phenotypic information.
Sequence Read Archive (SRA) contains vast next-generation sequencing (NGS) data but is inaccessible to common users.

Purpose of the Study:

To create an accessible platform for querying human NGS data and associated attributes from the SRA.
To provide a user-friendly web service and API for clinicians and researchers.
To overcome limitations of existing genomic databases by integrating phenotype data.

Main Methods:

Developed a pipeline using SRAtoolkit to download raw human NGS data from SRA.
Preprocessed data using the GATK pipeline.
Stored data in a cloud data lake for efficient access via a REST API and website.

Main Results:

Generated GeniePool, a web service and API for querying NGS data from SRA.
Enables direct access to information on samples and related studies.
Provides significant advantages over existing databases for clinical and research use.

Conclusions:

GeniePool is a multi-purpose tool leveraging data lake infrastructure for diverse clinical and research applications.
The platform offers a simple and intuitive way to explore metadata for daily clinical practice and research endeavors.
GeniePool enhances the utility of SRA data for the scientific community.