THIS IS A BIOINFORMATICS ASSIGNMENT Exercise 1 SHOW ALL WORK

THIS IS A BIOINFORMATICS ASSIGNMENT

Exercise #1. SHOW ALL WORK below to receive full credit; in other words, do not just write the final answer without showing an appropriate number of the calculations which were done.

1. What is the probability that the following sequence will occur in a genome in which all four bases are used with equal probability?

GGCAAACAACTC

2. What is the probability that a single point mutation occurring in the codon ATA will cause an amino acid change? Assume the standard genetic code and equal likelihood of each possible point mutation.

3. If the probability of mutation in a given virus is 1 X 10^-3 mutations per site per generation, what is the expected number of mutations per generation if the genome contains 1,000 bp? (An expectation is what you would expect the outcome of an experiment to be on average).

4. The human nuclear genome is approximately 3 billion base pairs in size. It is common to have a particular DNA sequence, known as a TATA box, upstream of protein-coding genes. It’s a signal of where to start transcription. The TATA box usually has this sequence: 5’-TATAAA-3’. How many of these sequences would you expect to find in the human genome? An approximation is acceptable as long as the work is shown below. (When calculating the expectation, you may assume that the calculation is performed with non-overlapping windows across the genome; therefore, there would be 500 million regions which could contain a 6-nucleotide motif)

Solution

1) Human genome contains about 3 billion of the base pairs. (3 x 10^9)

Now given sequence: GGCAAACAACTC

Probability of occurring for each base is 0.25 (as four bases (A,T,G,C = all have equal probability)

Chance of finding a 12bp (there are 12 base pairs in the given sequence) = (0.25)^12