Lecture 4 - K-mers and binomial and CLT

Question 1

What is a kmer?

Answer 1

a sequence of k bases

Question 2

when stored in binary a 32 bit integer holds how many k-mers?

Answer 2

16 base k-mer

Question 3

What is the probability of a specific kmer being generate by the RNG?

Answer 3

Kpi

Question 4

What is the conditional probability of an event A happening given an event B happens?

Answer 4

Pr A given B = P (AnB)/PB

Question 5

What is a context dependent nucleotide generator?

Answer 5

the probability of observing a particular nucleotide sequence depends on what the nucleotide was before it

Question 6

How do you model a context dependent random nucleotide generator?

Answer 6

Question 7

Given a genome of size n how can we test if the bases are generate randomly i.i.d or through a Markov process?

Answer 7

-calculate the expected number of times each dinucleotide is expected to appear in the genome
-calculate the frequency of each nucleotide use this to estimate the probability of each base
-calculate the probability of each nucleotide
-calculate the expected number of times each dinucleotide should appear in the genome
-count the number of times each dinulceotide appears in the genome
-compare the number of observed counts of each dinulceotide expected using the chi squared test - how many degrees of freedom

Question 8

What is the distribution of counts of an outcome?

Answer 8

Question 9

If n=4 and one outcome is 0110, how many different outcomes have zero 1s?

Answer 9

one

Question 10

If n=4 and one outcome is 0110, how many different outcomes have two 1s?

Answer 10

4C2