Transcript 5.genome-browsers

Bioinformatics Workshop 2
Identifying Unknown Genes …
• Open a web browser and type in the URL:
– informatics.gurdon.cam.ac.uk/online/workshops
– Bookmark this page
• Click on the link to the file:
– useful-websites.html
– Bookmark this page too
– It also contains links to the example sequence
files used in the workshop, and the
presentations themselves
Genome Browsers
Now that most model organisms have had their genomes sequenced, we
can get a lot more information about how the gene works, than by just
doing a BLAST search against the protein databases.
Even if ‘your’ favourite genome is still just in ‘scaffolds’ and not yet
assembled into chromosomes, we can still add a lot of value.
The main tasks that one does to a genome before releasing it to the user
community is to annotate it. In practice this means adding gene models,
based on known expressed sequences, both in the same organism and
other fairly closely related ones, and possibly also purely predicted ones
based on sequence composition analysis and ‘features’ like start and stop
codons, and splice sites. And then known mapping markers, SNPs, etc, etc.
With ~3,000,000,000 nucleotides in the genome sequence (human) this
present a considerable challenge to display on a web browser page, which
is of course the preferred option. Most genome browsers (software
designed to display genome based data in a web broswer) have taken
roughly the same approach, which we’ll take a quick look at…
Gene model
gene model
genome
Aligned cDNA
Aligned ESTs
Schematic Genome Browser
Mus musculus, chromosome 12
navigate
24000
genome
TRACKS
Your sequence
Genes
ESTs
25000
26000
zoom
+
27000
How to Use UCSC Browser
1.
Exercises
Find the web site for the Santa Cruz Genome Browser (sometimes called the
Golden Path), and investigate the three genes for which you have the full length
cDNA sequence, or the protein sequence, in the file
example-sequences.html
>TNeu084i05
How many exons does the gene appear to have?
Has it been mapped already?
Are there any likely upstream regulatory elements (look for conservation across
species)?
Are there other genes near by?
>TGas122d03
Is this a relatively unique gene, or a member of a gene family?
What can we learn from the comparison with human genes?
Are there any differences between the gene model predicted from your cDNA,
and the existing predictions?
>hsp70-5
Starts with the protein sequence. How might this be better?
Exercise 1. Results >TNeu084i05
Exercises
2.
Now go to the two other main genome browsers, Ensemble and NCBI –
find the Xenopus genome, and see if you get the same sort of functionality
from them. Use the same two sequences.
Are there different features?
Are they easier/harder to use?