Become aware of genome browser resources with this introductory tutorial. Genome browsers organize tremendous volumes of genome sequence data, adding context to genomic sequence with many types of annotations. Several major genome web browsers are widely used to search, retrieve, and display genome information for human and numerous other species. Here we introduce Ensembl, Map Viewer, UCSC Genome Browser, and the Integrated Microbial Genomes (IMG) browser. We also introduce the GBrowse software system, which is the framework for many additional genome browsers. Biomedical researchers need to be aware of these resources and be able to access the data available within.

You will learn:

  • where to find these useful tools
  • an overview of the organization and display features
  • some guidance on how or why to choose a given browser for your research needs
TUTORIAL RELATED CONTENT

TUTORIALS

This tutorial is a part of the tutorial group Genome Browsers. You might find the other tutorials in the group interesting:

Ensembl: Ensembl Genome Browser

Integrated Microbial Genomes (IMG): IMG is a powerful community resource for the comparative analysis and annotation of microbial genome data.

GBrowse: GBrowse User Introductory Tutorial

Ensembl Legacy: Older version of Ensembl Genome Browser

Map Viewer: Map Viewer Genome Browser from NCBI

CATEGORIES

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

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

BLOG POSTS

Video Tip of the Week: ZBrowse for GWAS viewing and exploration: Maybe you've heard of the others. ABrowse. BBrowse. CBrowse. GBrowse has been widely adopted. JBrowse is picking up steam. Into the orderly arrangement we now throw ZBrowse: a new way to look at genom...

Friday SNPpets: This week's SNPpets include tidbits about the Exome Aggregation Consortium (ExAC), new RepeatMasker track at UCSC Genome Browser, sequencing undiagnosed patients, the African Genome Variation Project, ...

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...

Video Tip of the Week: Centralized Model Organism Database (CMOD): This week's Tip of the Week is a bit different. The database resource that's the focus of this piece doesn't exist yet. Parts of it do, but there's a ways to go before we actually have a Centralized Mo...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Pousada Guillermo et al., Molecular and clinical analysis of TRPC6 and AGTR1 genes in patients with pulmonary arterial hypertension. Orphanet Journal of Rare Diseases (2015) doi:10.1186/s13023-014-0216-3

Zhang Li et al., The TLR7 agonist Imiquimod promote the immunogenicity of msenchymal stem cells. Biological Research (2015) doi:10.1186/0717-6287-48-6

Nguyen Van-Nui et al., Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities Selected articles from the Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015): Bioinformatics The Thirteenth Asia Pacific Bioinformatics Conference (APBC 2015). BMC Bioinformatics (2015) doi:10.1186/1471-2105-16-S1-S1

Chen Dongquan et al., Gene expression profile of human lung epithelial cells chronically exposed to single-walled carbon nanotubes. Nanoscale Research Letters (2015) doi:10.1186/s11671-014-0707-0

Gerek Z Nevin et al., Evolutionary Diagnosis of non-synonymous variants involved in differential drug response Selected articles from the 2nd International Genomic Medicine Conference (IGMC 2013): Medical Genomics 2nd International Genomic Medicine Conference (IGMC 2013). BMC Medical Genomics (2015) doi:10.1186/1755-8794-8-S1-S6