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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...

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....

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...

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...

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.

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Related Experiment Video

Updated: Apr 17, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Online resources for genomic analysis using high-throughput sequencing.

Daniel Blankenberg¹, James Taylor², Anton Nekrutenko¹

¹Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802;

Cold Spring Harbor Protocols

|February 7, 2015

Summary

This summary is machine-generated.

High-throughput sequencing generates vast data, causing an informatics bottleneck. This study details genomic data file formats and open-source tools for next-generation sequencing (NGS) analysis to aid researchers.

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

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Published on: May 23, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

High-throughput sequencing technologies have revolutionized biological research, generating unprecedented volumes of data.
The rapid increase in sequencing data presents significant informatics challenges, creating a bottleneck in data analysis and interpretation.
Many researchers face difficulties utilizing existing computational tools for complex next-generation sequencing (NGS) data analysis.

Purpose of the Study:

To address the informatics bottleneck in genomic data analysis.
To provide researchers with practical guidance on managing and analyzing large sequencing datasets.
To enhance the accessibility and usability of NGS data analysis tools and resources.

Main Methods:

Description of common file formats used for coding and storing genomic data.
Review of web-accessible, open-source resources for visualizing and analyzing NGS data.
Inclusion of practical examples and exercises for typical genomic data analyses.

Main Results:

Clarification of essential genomic data file formats for efficient data handling.
Identification of valuable open-source bioinformatics tools and platforms for data analysis.
Demonstration of common NGS data analysis workflows with actionable examples.

Conclusions:

Effective management of genomic data formats is crucial for overcoming analysis bottlenecks.
Leveraging open-source resources and community platforms can significantly empower researchers in NGS data analysis.
Practical examples and exercises facilitate the adoption and application of bioinformatics tools by a wider research community.