Here is a set of homologous sequences from three different p…
Here is a set of homologous sequences from three different primates for a gene responsible for the higher intelligence observed in primates. We are interested in understanding where transcription factors bind upstream of the gene so that we can attempt to modulate the expression of the gene in individuals with decreased cognition in a highly experimental treatment (i.e., this would never work in reality). We discussed several different approaches for finding motifs in sequences. The sequences are reprinted for each question that requires you to use the sequences. GTTCAG AATCAG TATTCG Use the GibbsSampler to find motifs for these sequences. Assume you are looking for 4-mers and work your algorithms so there’s never a 4-mer with zero probability in your matrix. If there is a random component to an algorithm, make sure you tell me what the “random” choice is and make sure that it is evident to me that you understand what random means in the context of the Gibbs Sampler (i.e., if there is a random component, explain it to me in words and demonstrate its appropriate use). Explain the difference between random starts and iterations. Why do we need both? Are they both trying to do the same thing? If it is helpful for you to make your points, you are welcome to use a figure, for example, a figure of the solution space you draw. For this question, use two random starts for two iterations each. Make sure you report the score for each set of motifs. If you don’t provide sufficient detail for me to see that you understand what to do, your writing is too messy to read, or the different steps are scattered across the page, giving you credit will be challenging.