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: 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 ...

Video Tip of the Week: UCSC #Ebola Genome Portal: Although I had other tips in my queue already, over the last week I've seen a lot of talk about the new Ebola virus portal from the UCSC Genome Browser team. And it struck me that researchers who have ...

Bioinformatics tools extracted from a typical mammalian genome project [supplement]: This is Table 1 that accompanies the full blog post: Bioinformatics tools extracted from a typical mammalian genome project. See the main post for the details and explanation. The table is too long to ...

Bioinformatics tools extracted from a typical mammalian genome project: In this extended blog post, I describe my efforts to extract the information about bioinformatics-related items from a recent genome sequencing paper, and the larger issues this raises in the field. It...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Kim Seon Dong et al., The acquisition of novel N-glycosylation sites in conserved proteins during human evolution Comparative genomics. BMC Bioinformatics (2015) doi:10.1186/s12859-015-0468-5

Naseer Muhammad Imran et al., Genome wide analysis of novel copy number variations duplications/deletions of different epileptic patients in Saudi Arabia Selected articles from the 2nd International Genomic Medicine Conference (IGMC 2013): Genomics 2nd International Genomic Medicine Conference (IGMC 2013). BMC Genomics (2015) doi:10.1186/1471-2164-16-S1-S10

Mills D James et al., High expression of long intervening non-coding RNA OLMALINC in the human cortical white matter is associated with regulation of oligodendrocyte maturation. Molecular Brain (2015) doi:10.1186/s13041-014-0091-9

Zhang Lu et al., Exome Sequencing of Normal and Isogenic Transformed Human Colonic Epithelial Cells (HCECs) Reveals Novel Genes Potentially Involved in the Early Stages of Colorectal Tumorigenesis Selected articles from the 2nd International Genomic Medicine Conference (IGMC 2013): Genomics 2nd International Genomic Medicine Conference (IGMC 2013). BMC Genomics (2015) doi:10.1186/1471-2164-16-S1-S8

Siggens Lee et al., Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions. Epigenetics Chromatin (2015) doi:10.1186/1756-8935-8-4