Introduction to genome browsers

Last updated on 2025-12-22 | Edit this page

Estimated time: 20 minutes

Overview

Questions

  • What are genome browsers and why are they useful?
  • How was the human reference genome constructed?

Objectives

  • Understand the utility of genome browsers
  • Describe the human reference genome

Introduction to genome browsers

Genome browsers are invaluable for viewing and interpreting the many different types of data that can be anchored to genomic positions. These include variation, transcription, the many types regulatory data such as methylation and transcription factor binding, and disease associations. The larger genome browsers serve as data archives for valuable public datasets facilitating visualisation and analysis of different data types. It is also possible to load your own data into some of the public genome browsers.

By enabling viewing of one type of data in the context of another, the use of Genome browsers can reveal important information about gene regulation in both normal development and disease, and assist hypothesis development relating to genotype phenotype relationships.

Callout

COMMONLY USED GENOME BROWSERS

All researchers are encouraged to become familiar with the use of some of the main browsers, such as:

These browsers are designed for use by researchers without programming experience and the developers often provide extensive tutorials and cases studies demonstrating the many ways in which data can be loaded and interpreted to assist in develop and supporting your research hypothesis.

Many large genomic projects also incorporate genome browsers into their web portals to enable users to easily search and view the data. These include:

The human reference genome

Genome browsers rely on a common reference genome for each species in order to map data from different sources to the correct location. A consortium has agreed on a common numbering for each position on the genome for each species. However, this position will vary based on the version of the genome, as error correction and updates can change the numbering. Therefore it is very important to know which version of the genome your data of interest is aligned to.

The sequence for the human reference genome was accumulated up over many years from sequence data from many different sources and does not represent the sequence of one single person. Instead it is a composite of fragments of the genome from many different people. Also, unlike the human genome which is diploid, the human reference genome is haploid. This means there is only one copy of each chromosome. Therefore, the human reference genome does not reflect the variation of the population, or even the most common variants in the human genome. Exploring variation within human genome is very important and facilitated by genome browsers but not covered in this workshop.

If you would like to learn more about genome build version number and updates, please go to:


Key Points
  • Genome browsers allow us to interpret and view many different types of data associated with genomic positions. They are designed to be used by researchers without programming experience.
  • Genome browsers rely on a common reference genome for each species to map data to the correct location.