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
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 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."
"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
1. Exploring features related to a gene
- (a) Search for the human TAC1 gene by typing 'human TAC1 gene' in the
- (b) How many transcripts are predicted for this gene? What is the size of the
longest predicted mRNA? How many exons does it have? How many amino
acids does it code for?
What is a possible function of TAC1?
- (d) Which domains does the protein product contain?
- (e) Find the GO section and follow some of the links to explore
the 'Gene ontology' terms (describing gene and protein function).
- (f) In which chromosomal band and on which clone and contig in the genomic
sequence assembly is the TAC1 gene located?
- (g) Is there a putative mouse orthologue? If so,
where is it in the mouse genome?
- 2. Exploring a region
- (a) Display the region between markers D12S764 and D12S1871. Start on the human homepage, and click on chromosome 12.
- (b) What is the closest marker to the TENC1 gene? How many synonyms
does this marker have?
- (c) Zoom in (towards the '+') on the zoom triangle and turn on the
SNP track. Identify an intronic SNP and look at the corresponding SNP information
- 3. Exploring the zebrafish (Danio rerio) genome with Ensembl
- (a) Bring up a display of zebrafish (Danio rerio) chromosome 1
between 54.0 Mb and 54.5 Mb.
- (b) How many 'known' and 'novel' genes are predicted in this region? For one
of the known genes, find some information about its function, and look at an
entry for it in EntrezGene, UniProt/Swiss-Prot or the ZFIN site (ZFIN.org).
- (c) Can you find out anything about the possible functions of one of the novel
genes? For this, try looking at homologues in other species, at other members
of protein families and domains.
Part III. Browsing Genome data in UCSC
UCSC Genome Browser introduction. [PPT]
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
- 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.
Ensembl - Short Videos
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,
- Online Tutorial