Learn to use tools associated with the UCSC Genome Browser with this free tutorial, sponsored by UCSC Genome Bioinformatics Group. The UCSC Genome Browser provides other tools beyond genome browsing and querying that may be useful to your research. This third tutorial in the UCSC Genome Browser series explores additional interfaces, access points and visualizations for various data types, all within the framework of the official genome reference sequences from many species.

You will learn:

  • to use the clever Gene Sorter to find relationships among genes
  • to perform in silico PCR to identify possible PCR products
  • to access ENCODE project data, including pre-publication material
  • to find protein data in the Proteome Browser
  • to explore image data with the VisiGene Browser
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: 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

UCSC Genome Browser: An Introduction: The UCSC Genome Browser Introduction

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.

Expression : This category may contain various expression data collections, annotation tools, or repositories of expression data.

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

Nucleotides : Tools that are primarily used in the storage, retrieval, or exploration of nucleotide-based data. Some tools may also involve protein sequence information.

Proteins : Tools that are primarily used in the storage, retrieval, or exploration of amino acid based data. Some tools may also involve nucleotide sequence information.

BLOG POSTS

Video Tip of the Week: Viewing Amino Acid info in the UCSC Genome Browser: We've been doing training on the UCSC Genome Browser for over 10 years now. We've seen it grow from just a few genomes and a few tracks to the enormous trove of information it is today. In fact, one of...

Customizing Your Digital Research Environment with Genome Browsers, #BioIT15: Every time we do a workshop on genome browser tools and other associated resources, we find that there's someone who's shocked to discover how much they didn't realize was underneath the interface. One...

Video Tip of the Week: The New OpenHelix Interface: Generally we like to highlight new features and new tools from bioinformatics software providers. But this week we wanted to introduce some new features of our own OpenHelix site. If you've been using ...

Video Tip of the Week: Aquaria, streamlined access to protein structures for biologists: This week's Video Tip of the Week is Aquaria, a new resource for exploring protein structures, mutations, and similarities to other proteins. It's a very well-designed and interactive experience for en...

Video Tip of the Week: Genome Browser in a Box: We've been doing UCSC Genome Browser training workshops for a decade now. We've seen all sorts of situations--from places that had terrific bioinformatics and IT support, to places where the attendees ...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Huang Jie et al., Genome-wide survey and analysis of microsatellites in giant panda ( Ailuropoda melanoleuca ), with a focus on the applications of a novel microsatellite marker system. BMC Genomics (2015) doi:10.1186/s12864-015-1268-z

Castellano Leandro et al., The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs. BMC Genomics (2015) doi:10.1186/s12864-015-1257-2

González García Ramón Juan et al., Are submicroscopic chromosomal inversions predisposing factors for the t(9;22)(q34;q11.2) translocation in chronic myeloid leukemia?. Molecular Cytogenetics (2015) doi:10.1186/s13039-015-0116-9

Dobek A Whitney et al., Long-term follow-up of females with unbalanced X;Y translocations—reproductive and nonreproductive consequences. Molecular Cytogenetics (2015) doi:10.1186/s13039-015-0112-0

Fleming D Joseph et al., STAT3 acts through pre-existing nucleosome-depleted regions bound by FOS during an epigenetic switch linking inflammation to cancer. Epigenetics Chromatin (2015) doi:10.1186/1756-8935-8-7