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

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

Kumar Sunil et al., Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features. BMC Bioinformatics (2016) doi:10.1186/s12859-015-0846-z

Mazzoccoli Gianluigi et al., Deregulated expression of cryptochrome genes in human colorectal cancer. Molecular Cancer (2016) doi:10.1186/s12943-016-0492-8

Watson M. Christopher et al., Enhanced diagnostic yield in Meckel-Gruber and Joubert syndrome through exome sequencing supplemented with split-read mapping Clinical-Molecular Genetics and Cytogenetics. BMC Medical Genetics (2016) doi:10.1186/s12881-015-0265-z

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

Al-Yacoub Nadya et al., FBXO32 , encoding a member of the SCF complex, is mutated in dilated cardiomyopathy. Genome Biology (2016) doi:10.1186/s13059-015-0861-4