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

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...

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.

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...

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.

GIS Software, Hardware, and Sources of GIS Data

GIS Software, Hardware, and Sources of GIS Data

A Geographic Information System (GIS) combines specialized software and hardware to effectively manage, analyze, and present spatial and related data. GIS software includes critical functionalities such as a user interface for easy navigation, database management tools for handling spatial and attribute data, and data retrieval features for efficient access. Analytical tools transform raw data into insights, while display functions produce maps and reports in various formats for effective...

Statgraphics

Statgraphics

Statgraphics is a comprehensive statistical software suite designed for both basic and advanced data analysis. Originating in 1980 at Princeton University under Dr. Neil W. Polhemus, it was one of the pioneering tools for statistical computing on personal computers, with its public release in 1982 marking an early milestone in data science software. Over the years, it has evolved into a robust platform for data science, offering tools for regression analysis, ANOVA, multivariate statistics,...

You might also read

Related Articles

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

Sort by

Same author

Molecular features unique to circulating tumor DNA enable the tumor-naïve liquid biopsy of glioblastoma.

NPJ precision oncology·2026

Same author

Obesity promotes conserved inflammatory and metabolic transcriptional programs in colon tumors: evidence from mouse models and the ColoCare Study Patient Cohort.

The American journal of clinical nutrition·2025

Same author

Germline whole-exome sequencing reveals <i>FOXP3</i>-related gene variants conferring urinary cancer susceptibility and associated with immune escape.

Journal for immunotherapy of cancer·2025

Same author

Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race.

Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology·2025

Same author

Obesity promotes conserved inflammatory and metabolic transcriptional programs in mouse and human colon tumors.

bioRxiv : the preprint server for biology·2025

Same author

Dramatic Responses to High-Dose Ipilimumab Plus Temozolomide After Progression on Standard- or Low-Dose Ipilimumab in Advanced Melanoma.

Current oncology (Toronto, Ont.)·2025

Same journal

Covariance decomposition for distance based species tree estimation.

BMC bioinformatics·2026

Same journal

SNPio: a Python interface for population genomic data processing.

BMC bioinformatics·2026

Same journal

SpaHNR: a spatial domain identification method via sparse attention-based hierarchical node representation and multi-view contrastive learning.

BMC bioinformatics·2026

Same journal

OpenIMC: an open-source platform for analyzing single-cell and spatial proteomics by imaging mass cytometry.

BMC bioinformatics·2026

Same journal

NAP: an open source pipeline for cross-domain microbiome profiling using Nanopore sequencing-derived amplicon data.

BMC bioinformatics·2026

Same journal

SurvGME: an R package for survival analysis with graphical and measurement error models.

BMC bioinformatics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Jun 9, 2026

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

Next generation tools for genomic data generation, distribution, and visualization.

David A Nix¹, Tonya L Di Sera, Brian K Dalley

¹Department of Oncological Sciences, University of Utah, Huntsman Cancer Institute, Salt Lake City, USA. david.nix@hci.utah.edu

BMC Bioinformatics

|September 11, 2010

Summary

This summary is machine-generated.

Managing genomic data is crucial with advancing sequencing technologies. We developed three open-source tools (GNomEx, GenoPub, GWrap) for efficient genomic data analysis, distribution, and visualization.

More Related Videos

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Related Experiment Videos

Last Updated: Jun 9, 2026

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

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Introductory Analysis and Validation of CUT&RUN Sequencing Data

Published on: December 13, 2024

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput sequencing and microarray technologies are increasingly accessible.
Genomic data management, analysis, and sharing present a significant bottleneck.
Efficient tools are needed to leverage the potential of genomic data.

Purpose of the Study:

To present three open-source, platform-independent software tools.
To facilitate the generation, analysis, distribution, and visualization of genomic data.
To address the challenges in managing and sharing complex genomic information.

Main Methods:

Developed GNomEx: a LIMS and analysis project center for next-generation sequencing/microarray data.
Developed GenoPub: an application for annotating and distributing genomic data via DAS/2 protocol.
Developed GWrap: a Java Swing application providing GUI access to command-line analysis tools.

Main Results:

GNomEx and GenoPub utilize a Flex/Flash web interface, Java classes, and a relational database.
A public-private user-group security model allows controlled data distribution.
Tools enable manual and programmatic access to genomic data repositories, including through the Integrated Genome Browser.

Conclusions:

The developed software tools are widely used in core facilities, research labs, and clinics.
These tools are freely available for non-profit use.
The software facilitates efficient genomic data handling and analysis.