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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...

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...

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.

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...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

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Related Experiment Video

Updated: Mar 3, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

D3GB: An Interactive Genome Browser for R, Python, and WordPress.

David Barrios¹, Carlos Prieto^1,2

¹1 Bioinformatics Service, Nucleus, University of Salamanca (USAL) , Salamanca, Spain .

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|April 25, 2017

Summary

This summary is machine-generated.

D3 Genome Browser offers an interactive, web-shareable tool for visualizing genomic data. This tool enhances analysis pipelines, improving results and data quality through easy integration and broad format compatibility.

Keywords:

Python R WordPress genome browser next generation sequencing visualization

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Last Updated: Mar 3, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Published on: July 16, 2017

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Published on: December 7, 2021

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

Bioinformatics
Genomics
Data Visualization

Background:

Genome browsers are essential for visualizing genomic data and refining analysis protocols.
Integrating genome browsers into analysis pipelines optimizes parameters for improved results.
Advancements in genome browser development can enhance genomic data analysis and visualization.

Purpose of the Study:

To introduce D3 Genome Browser, an interactive tool for genomic data visualization.
To highlight its seamless integration into analysis pipelines and web-sharing capabilities.
To demonstrate its utility in improving analysis protocols and data quality.

Main Methods:

D3 Genome Browser is developed as an R package, Python module, and WordPress plugin for versatile integration.
It supports popular genomic data formats including GenBank, GFF, BED, FASTA, and VCF.
The browser enables interactive exploration of genomic data directly within a web browser.

Main Results:

Facilitates easy integration into existing bioinformatics workflows and analysis pipelines.
Enables rapid visualization and exploration of diverse genomic datasets.
Supports parameter optimization within analysis protocols, leading to enhanced results.

Conclusions:

D3 Genome Browser provides a flexible and accessible platform for genomic data visualization and analysis.
Its multi-platform distribution and format compatibility streamline bioinformatics workflows.
The tool contributes to improved genomic data quality and faster generation of analysis results.