We are going to look at two public genome browsers:
- EBI's Ensembl
- the UCSC Genome Browser (European mirror)
- Are there any vertebrates that are only found in one of the two browsers?
- Looking for the human HBB gene (hemoglobin, beta) in the UCSC browser will bring up a 1,606 bp region (UCSC Genes track). Searching for HBB in Ensembl leads to a region nearly 4 kb in size. Can you explain the difference?
- Try to find out which tissue the following genes are mostly expressed in. Compare results between the two browsers:
- Here is an excerpt from a paper on blue eye color in humans:
"In total, all these data strongly suport a model where the blue
eye color in humans is caused by homozygosity of the
Find out which of the resequenced individuals (available in Feb 2014 archive) might have blue eyes. Can you confirm your findings through a Google image search?
- See Eupedia for a list of addiction-related SNPs. Which individuals might be at risk of nicotine/cocaine/cannabis dependence?
- Select the 2006 version of the fruit fly (dm3) in UCSC and upload a custom track in BED format (URL: http://bioinf.gen.tcd.ie/GE3M25/bioinformatics/Weederh_and_RedFly.bed) with TFBS predictions from WeederH and experimentally verified TFBSs from the RedFly database. How do they match up with conserved regions and ChIP peaks?