Clock Gene Analysis- 2 mins
For this project, my partner and I did an analysis of the clock gene (Dmel/Clk) found on the third chromosome of Drosophilla Melanogaster (the fruit fly).
Our research involved determining the function of the clock gene and how it is affected by different stimuli such as light and comparing the gene and amino acid sequences of the fruit fly with those of other organisms (The Red Junglefowl, The typical House Mouse, The Brown Rat, The Giant River Prawn and the Firebrat).
We utilized the Multiple sequence alignment tool by Florence Corpet to align the clock genes and amino acid of the different organisms. This provided a clear view of the areas of high and low sequence matches. However, we were interested in the exact percentages of not just the high an low consensus areas but the areas of the gene with medium and no consensus at all. For this we used the Multiple Sequence Comparison by Log-Expectation (MUSCULE) system. The report it generated marked the areas we were interested in with different symbols that allowed us to determine consensus frequency variations in the gene versus the protein using good Google Chrome features and a calculator. We then created a rotating 3-D model of the different motifs using PyMOL.
Our analysis led us to conclude that there is more variation in the protein versus the gene and the clock gene affects organisms differently, with and mutations in the gene resulting in unique changes in the rhythmic activities of the organisms.
Some pictures detailing portions of our analysis can be found below:
|Area with Highest Concentration of Gene Alignments|
|Area with Highest Concentration of Amino Acid Alignments|
|Consensus Frequency in the Gene|
|Consensus Frequency in the Amino Acid|
|3-D Model of Amino Acid Interaction with DNA|