An introduction to the UCSC Genome Browser

Raymond Lee

doi:10.1895/wormbook.1.160.1

Abstract

The Genome Browser at the University of California Santa Cruz provides a uniform graphical interface to sequences, features, and annotations of genomes across a wide spectrum of organisms, from yeast to humans. In particular, it covers seven nematode genomes: Caenorhabditis elegans, C. sp. 11, C. brenneri, C. briggsae, C. remanei, C. japonica, and Pristionchus pacificus and thus is particularly useful for multiple-genome comparative analysis. One can use the provided tools and visual aides to facilitate sequence feature detection and examination. This article provides a brief introduction for using the Genome Browser from the perspective of a C. elegans researcher. Interested users should read the official user guide and explore the site more deeply as there are many more features not mentioned here.

Highlights

Division of Biology, California Institute of Technology, Pasadena CA 91125, USA The Genome Browser at the University of California Santa Cruz provides a uniform graphical interface to sequences, features, and annotations of genomes across a wide spectrum of organisms, from yeast to humans
This article provides a brief introduction for using the Genome Browser from the perspective of a C. elegans researcher
On chromosome IV, between C48A7.14 and C48A7.13, there is a 530 bp region that is highly conserved between C. elegans and five other species but there is no existing annotation (Figure 2)

Summary

Introduction

Division of Biology, California Institute of Technology, Pasadena CA 91125, USA The Genome Browser at the University of California Santa Cruz provides a uniform graphical interface to sequences, features, and annotations of genomes across a wide spectrum of organisms, from yeast to humans. This article provides a brief introduction for using the Genome Browser from the perspective of a C. elegans researcher. One should choose the nematode clade, the organism C. elegans, a version of genome sequence assembly (e.g., WS220), and a region of the genome (Figure 1).

Results

Conclusion