Visualizing Genomic Annotations with the UCSC Genome Browser
Program in Bioinformatics and Integrative Biology; Department of Biochemistry and Molecular Pharmacology
Bioinformatics | Computational Biology | Genomics
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.
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Citation: Cold Spring Harb Protoc. 2016 Nov 1;2016(11):pdb.prot093062. doi: 10.1101/pdb.prot093062. Link to article on publisher's site
Cold Spring Harbor protocols
Hung, Jui-Hung and Weng, Zhiping, "Visualizing Genomic Annotations with the UCSC Genome Browser" (2016). Program in Bioinformatics and Integrative Biology Publications and Presentations. 94.