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

Video Tip of the Week: New UCSC Genome Browser Gateway look: For years now we've been doing training and outreach on the UCSC Genome Browser. And there's been a lot of change over the years--so much more data, so many new tools, new species. All that ENCODE inf...

Friday SNPpets: This week's SNPpets include something unusual: bioinformatics software becoming a mainstream discussion. A recent NYT piece about Zika genomics included a Bandage software-based illustrations, and a su...

Video Tip of the Week: Multi-region visualization in the UCSC Genome Browser: This week's video tip demonstrates a new feature at the UCSC Genome Browser. I think it's kind of unusual, and conceptually took me a little while to get used to when I started testing it. So I wanted ...

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...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Janssen G. Bram et al., Placental mitochondrial DNA and CYP1A1 gene methylation as molecular signatures for tobacco smoke exposure in pregnant women and the relevance for birth weight Disease Biomarkers. Journal of Translational Medicine (2017) doi:10.1186/s12967-016-1113-4

Cumbo Fabio et al., TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1419-5

Wingo S. Thomas et al., MPD: multiplex primer design for next-generation targeted sequencing Results and data. BMC Bioinformatics (2017) doi:10.1186/s12859-016-1453-3

Popitsch Niko et al., Temperature-dependent sRNA transcriptome of the Lyme disease spirochete Prokaryote microbial genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3398-3

Xu Chang et al., Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3425-4