UMass Chan Affiliations
Department of Biochemistry and Molecular PharmacologyProgram in Bioinformatics and Integrative Biology
Document Type
Journal ArticlePublication Date
2016-11-01
Metadata
Show full item recordAbstract
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.Source
Cold Spring Harb Protoc. 2016 Nov 1;2016(11):pdb.prot093062. doi: 10.1101/pdb.prot093062. Link to article on publisher's siteDOI
10.1101/pdb.prot093062Permanent Link to this Item
http://hdl.handle.net/20.500.14038/25953PubMed ID
27574198Related Resources
Link to Article in PubMedae974a485f413a2113503eed53cd6c53
10.1101/pdb.prot093062