Genome Browsers

In this class we will examine three genome browsers for human and other eukaryotic genomes. We have already covered some concepts about genomes and sequencing, so this module will focus more on extracting data from the genome maps.

Why do we care about Map Viewers:

1. Where does gene X exist within the genome of organism Y? What are some flanking markers?
2. Which genes exist on a chromosome, and in what order do they appear?
3. Show the genes that exist in region R of the chromosome. Show me the corresponding sequence data for that region.
4. Display the region of a chromosome between points A and B. Show both the cytogenetic and sequence map for that region, aligned to each other based on markers that have been placed on both maps.
5. What is the distance between two genes? (Note: scale depends on the type of map on which those genes have been placed.)
6. I know the cytogenetic location of gene X. What is the corresponding physical location?

For each browser we will look at:

1. Finding a region by a map position: 4q21.3
2. Finding a region by homology to a sequence
3. Synteny maps

1. NCBI map viewer
2. UCSC map viewer
3. ENSEMBL browser

HOMEWORK

The homework is online.