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Genomics

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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...

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Related Experiment Video

Updated: May 19, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

The UCSC genome browser and associated tools.

Robert M Kuhn¹, David Haussler, W James Kent

¹Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA. kuhn@soe.ucsc.edu

Briefings in Bioinformatics

|August 22, 2012

Summary

This summary is machine-generated.

The UCSC Genome Browser provides integrated genomic data visualization for 58 organisms, supporting diverse data types and high-throughput sequencing experiments. It facilitates data mining and sharing through tools like BLAT and Custom Tracks.

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Last Updated: May 19, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

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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
Data Visualization

Background:

The UCSC Genome Browser has been a key resource for genomic data visualization for over a decade.
It integrates diverse genomic datasets, including gene predictions, epigenomic data, and variation data.

Purpose of the Study:

To provide an updated overview of the UCSC Genome Browser's capabilities and features.
To highlight its utility for inquiry-driven data mining and analysis of large-scale sequencing data.

Main Methods:

Visualization of genomic annotations mapped to genomic coordinates for 58 organisms.
Integration of diverse data types including gene predictions, mRNA alignments, epigenomic data (ENCODE), conservation scores, and variation data.
Support for uploading private data via Custom Tracks and Data Hubs, and visualization of high-throughput sequencing data formats (BAM, VCF, SNP).

Main Results:

The Browser offers visualization from single base to entire chromosome scale.
Tools like BLAT, Table Browser, and Saved Sessions enhance data analysis and sharing.
Support for compact, indexed formats (BAM, bigBed, bigWig) enables rapid visualization of large datasets from RNA-seq and ChIP-seq experiments.

Conclusions:

The UCSC Genome Browser remains a comprehensive and versatile platform for genomic data exploration and analysis.
Its continuous development supports modern high-throughput sequencing and facilitates collaborative research through data sharing features.