Learn to use the UCSC Genome Browser with this free tutorial, sponsored by UCSC Genome Bioinformatics Group. The UCSC Genome Browser provides a way to examine the data from many genomes, with extensive annotation tracks for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more. This introductory tutorial focuses on the foundation and framework for the organization and display of the data, and basic text and sequence searches. This tutorial, which is the first in a series of three tutorials on the UCSC Genome Browser, will get you on your way to expertly navigating this vital tool for genomic research.

You will learn:

  • to perform basic text searches on the UCSC Genome Browser
  • to understand and customize the displays in genomic regions of interest
  • to access additional details and sequence data
  • to start with a sequence and find genomic regions of interest using BLAT
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group UCSC Tutorials. You might find the other tutorials in the group interesting:

ENCODE Foundations: ENCyclopedia of DNA Elements

UCSC Genome Browser: The Additional Tools: Additional tools at the UCSC Genome Browser

UCSC Genome Browser: Custom Tracks and Table Browser: UCSC Genome Browser advanced topics

UCSC Archaeal Genome Browser: Provides you with many research and analysis tools that can be used to examine the genomes of more than 50 microbial species from the domain archaea.

ENCODE Data at UCSC: ENCODE Data at UCSC

CATEGORIES

Algorithms and Analysis : This category contains various tools that may help perform analysis of different genomics data types. This may include sequence alignment, large-scale or complex queries, motif finding, or comparative assessments.

Genome Databases (euk) : Genomic databases or repositories primarily aimed at eukaryotic organisms. Some may contain prokaryotic data as well.

BLOG POSTS

Friday SNPpets: This week's SNPpets cover a range of issues. Attempting to community-curate bioinformatics tools, a new paper on UCSC Genome Browser's features, iPlant now reborn as CyVerse, errors in databases, perso...

Video Tip of the Week: UniProt updates, now including portable BED files: UniProt is one of the core resources that provides tremendously important curated information about proteins. You will find links to UniProt in lots of other tools and databases as well, but we've alwa...

Friday SNPpets: This week's SNPpets offer a nutty new genome and a pine (just like pretty much every day of the week lately there are new genomes). Legal obstacles to data sharing, again. The TL;DR statement on human ...

Video Tip of the Week: Send UCSC Genome Browser sequence to external tools: The folks at the UCSC Genome Browser are always adding new features, new data, and new genomes to their site. And although they use the genome-announce mailing list to get the word out, even I can miss...

Video Tip of the Week: UCSC Table Browser and Custom Tracks: This week's video tip is longer than usual. But if you want to dig deeper into all the data that you know is coming in to the UCSC Genome Browser, you want to use the Table Browser. If you've only used...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Grevendonk Lotte et al., Mitochondrial oxidative DNA damage and exposure to particulate air pollution in mother-newborn pairs. Environmental Health (2016) doi:10.1186/s12940-016-0095-2

Watson T. Corey et al., Genome-wide12 DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer’s disease. Genome Medicine (2016) doi:10.1186/s13073-015-0258-8

Zhang Wanchang et al., Genetic architecture of fatty acid composition in the longissimus dorsi muscle revealed by genome-wide association studies on diverse pig populations. Genetics Selection Evolution (2016) doi:10.1186/s12711-016-0184-2

Parikh Hemang et al., svclassify: a method to establish benchmark structural variant calls Human and rodent genomics. BMC Genomics (2016) doi:10.1186/s12864-016-2366-2

Vad-Nielsen Johan et al., Regulatory dissection of the CBX5 and hnRNPA1 bi-directional promoter in human breast cancer cells reveals novel transcript variants differentially associated with HP1α down-regulation in metastatic cells Cell and molecular biology. BMC Cancer (2016) doi:10.1186/s12885-016-2059-x