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

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: JBrowse at Araport: The JBrowse genome browser has been around for a long time now. In fact, our first mention of it on the blog was in 2009, apparently. But we've talked about it a number of times since as it continued t...

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...

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: PanelApp, from the 100000 Genomes Project: Genomics England is responsible for the 100,000 Genomes Project Last week I talked about the 100,000 Genomes Project in the UK. That video tip was an introduction and overview of the project. This wee...

BIOMED CENTRAL

Recent BioMed Central research articles citing this resource

Janssen G. Bram et al., Placental mitochondrial DNA and CYP1A1 gene methylation as molecular signatures for tobacco smoke exposure in pregnant women and the relevance for birth weight Disease Biomarkers. Journal of Translational Medicine (2017) doi:10.1186/s12967-016-1113-4

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

Pfäfflin Frieder et al., Implementation of the WHO multimodal Hand Hygiene Improvement Strategy in a University Hospital in Central Ethiopia. Antimicrobial Resistance Infection Control (2017) doi:10.1186/s13756-016-0165-9

Piechotta Michael et al., JACUSA: site-specific identification of RNA editing events from replicate sequencing data Sequence analysis (applications). BMC Bioinformatics (2017) doi:10.1186/s12859-016-1432-8

Camponovo Flavia et al., Incidence and admission rates for severe malaria and their impact on mortality in Africa. Malaria Journal (2017) doi:10.1186/s12936-016-1650-6