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: 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

Niu Yuchun et al., Long non-coding RNA TUG1 is involved in cell growth and chemoresistance of small cell lung cancer by regulating LIMK2b via EZH2. Molecular Cancer (2017) doi:10.1186/s12943-016-0575-6

Eslami Rasekh Marzieh et al., Discovery of large genomic inversions using long range information Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3444-1

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

Sacco James et al., Polymorphisms in the canine monoamine oxidase a ( MAOA ) gene: identification and variation among five broad dog breed groups. Canine Genetics and Epidemiology (2017) doi:10.1186/s40575-016-0040-2

Sahakyan Aleksandr B. et al., Single genome retrieval of context-dependent variability in mutation rates for human germline Human and rodent genomics. BMC Genomics (2017) doi:10.1186/s12864-016-3440-5