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The UCSC Genome Browser Introduction

Tutorial and training materials by OpenHelix

Learn to use the UCSC Genome Browser with this free tutorial, sponsored by UCSC Genome Bioinformatics Group. The UCSC Genome Browser provides a way to examine the data from many genomes, with extensive annotation tracks for various data types including known genes, predicted genes, SNPs, comparative multi-species analysis and much more. This introductory tutorial focuses on the foundation and framework for the organization and display of the data, and basic text and sequence searches. This tutorial, which is the first in a series of three tutorials on the UCSC Genome Browser, will get you on your way to expertly navigating this vital tool for genomic research.
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You'll learn:

  • to perform basic text searches on the UCSC Genome Browser
  • to understand and customize the displays in genomic regions of interest
  • to access additional details and sequence data
  • to start with a sequence and find genomic regions of interest using BLAT


Related tutorials

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


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

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Recent BioMed Central research articles citing this resource

Ebert Grit et al., Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7 Human and rodent genomics. BMC Genomics (2014) doi:10.1186/1471-2164-15-537

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

Diroma Maria Angela et al., Extraction and annotation of human mitochondrial genomes from 1000 Genomes Whole Exome Sequencing data Italian Society of Bioinformatics (BITS): Annual Meeting 2013: Genomics Tenth Annual Meeting of the Italian Society of Bioinformatics (BITS). BMC Genomics (2014) doi:10.1186/1471-2164-15-S3-S2

Silverman M Ian et al., RNase-mediated protein footprint sequencing reveals protein-binding sites throughout the human transcriptome. Genome Biology (2014) doi:10.1186/gb-2014-15-1-r3

Hudson J Nicholas et al., Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest Comparative genomics. BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-66

More about the resource:

The UCSC Genome Browser, sometimes referred to as the "Golden Path" browser, offers a well-organized and user-friendly view of the human genome, along with dozens of other genomes as well. The official genomic sequence is supplemented with many other data types which are useful to researchers: expression, variation, comparative genomics, and many more. The data can be accessed with simple text or sequence searches using BLAT, or probed in depth with customized queries. Be sure to see the other UCSC tutorials for advanced topics and additional tools as well.


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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.
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