P13: Genome Browsers

In this practical class we will learn which are the main features of the three main Genome Browsers. We will learn how to use basic functions of the Ensembl Genome Browsers

Toni Gabaldon

Part I. Three main genome browsers

UCSC Genome browser:
"This site contains the reference sequence and working draft assemblies for a large collection of genomes. It also provides a portal to the ENCODE project."

Ensembl:
"Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes."

Mapview NCBI:
"The NCBI Map Viewer provides graphical displays of features on the human genome sequence assembly as well as cytogenetic, genetic, physical, and radiation hybrid maps."

Overview of the three browsers

Slide presentation of the main features of the three Genome Browsers. [PDF]

Part II. Using Ensembl browser

Introduction to Ensembl. [ON-LINE]

Ensembl - Excersises

Part III. Browsing Genome data in UCSC

UCSC Genome Browser introduction. [PPT]

UCSC Genome browser: http://genome.ucsc.edu/

UCSC Genome Browser Excersices

• 1) Find out if the mouse Brca1 gene has non-synonymous SNPs, color them blue, and get external data about a codon-changing SNP.
  Skills: basic text search; Genome Viewer pulldown menus; filters; links to external resources
  
  
• 2) Find the protein sequence for rat leptin. BLAT this sequence vs. the human genome to find the human homolog. Look for SNPs in the coding region of this gene—are there any? Obtain the human DNA sequence for this region, and underline the SNPs.
  Skills: obtaining protein sequence; BLAT; finding SNPs in exons "get DNA" sequence with extended case/color options
  
  
• 3) Find the genomic region for the human NRAS [neuroblastoma RAS viral (v-ras) oncogene homolog] gene. Add 1000 bases to each end of the position in the window. Turn on a Transcription Factor Binding Site (TFBS Conserved) track and look for possible binding sites in the promoter region. Determine if structural variation has been indicated in this genomic region by visualizing the copy number variation (CNV) data from the DGV database track.
  Skills: examining TFBS; Copy Number Variations.

Further Information

Ensembl - Short Videos

• Ensembl Worksops Online
  
  

Ensembl - Excersises

• Ensembl browser exercises. [PDF]
  
  

UCSC Genome Browser exercises - Excersises

• UCSC Genome Browser exercises [PDF] 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 2006, OpenHelix, LLC.
• Online Tutorial