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Various Genome Browsers examined

Tutorial and training materials by OpenHelix

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.
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You'll 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


Related tutorials

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

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Recent BioMed Central research articles citing this resource

Li Wentian et al., Diminishing return for increased Mappability with longer sequencing reads: implications of the k -mer distributions in the human genome Sequence analysis (methods). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-2

Dalmasso C María et al., Characterization of Toxoplasma gondii subtelomeric-like regions: identification of a long-range compositional bias that is also associated with gene-poor regions Eukaryote microbial genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-21

Manconi Andrea et al., A tool for mapping Single Nucleotide Polymorphisms using Graphics Processing Units Integrated Bio-Search: Selected Works from the 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012) Integrated Bio-Search: 12th International Workshop on Network Tools and Applications in Biology (NETTAB 2012). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-S1-S10

Kai Wataru et al., A ddRAD-based genetic map and its integration with the genome assembly of Japanese eel ( Anguilla japonica ) provides insights into genome evolution after the teleost-specific genome duplication Non-human and non-rodent vertebrate genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-233

Werner Andreas et al., Contribution of natural antisense transcription to an endogenous siRNA signature in human cells Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-19

More about the resource:

The Ensembl browser is provided by the Sanger Institute and the EBI. Map Viewer comes to you from the NCBI. UCSC Genome Browser is produced by the Genome Bioinformatics Group at UC Santa Cruz. Integrated Microbial Genome (IMG) is supported by the DOE Joint Genome Institute, US Department of Energy. GBrowse is an open-source software program developed by the Generic Model Organism Database (GMOD) .


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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