Title

Visualizing Genomic Annotations with the UCSC Genome Browser

UMMS Affiliation

Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology

Publication Date

11-1-2016

Document Type

Article

Disciplines

Bioinformatics | Computational Biology | Genomics

Abstract

Genomic data and annotations are rapidly accumulating in databases such as the UCSC Genome Browser, NCBI, and Ensembl. Given the massive scale of these genomic databases, it is important to be able to easily retrieve known data and annotations of a specified genomic locus. For example, for a newly identified cis-regulatory element bound by a transcription factor, questions that immediately come to mind include whether the element is near a transcriptional start site and, if so, the name of the corresponding gene, and whether the histones or DNA at the locus are modified. The UCSC Genome Browser organizes data and annotations (called tracks) around the reference sequences or draft assemblies of many eukaryotic genomes and presents them using a powerful web-based graphical interface. This protocol describes how to use the UCSC Genome Browser to visualize selected tracks at specified genomic regions, download the data and annotations for further analysis, and retrieve multiple sequence alignments and their conservation scores.

Rights and Permissions

Citation: Cold Spring Harb Protoc. 2016 Nov 1;2016(11):pdb.prot093062. doi: 10.1101/pdb.prot093062. Link to article on publisher's site

Related Resources

Link to Article in PubMed

Journal/Book/Conference Title

Cold Spring Harbor protocols

PubMed ID

27574198