Lecture 4 Flashcards
(32 cards)
Substution of a pyrimidine to a purine is called —, and pyrimidine/ purine to a different variant of itself is called —
transversion, transition
what are pyrimidines in DNA?
T and C
What are purines in DNA?
A and G
In the JC69 model with t reaching infinite amounts, how will the nucleotides bee distributed?
it reaches stationary distribution where any long sequence will be composed of equal amount of each nucleotide, no matter what the initial distribution was.
How do we express the likelihood of throwing x times a 6 out of n tries in a binomial distribution as a function?
slide 26 lecture 4
what is the log likelihood of the function above?
slide 26 lecture 4
How do we obtain a confidence interval based on log likelihood?
-we determine the value of the log likelihood function in parameter estimate l(estimate;x)
- we subtract 0.5 X2_k_5% from the found likelihood, we then determine those values for which the condition above holds for the likelihood of the parameter itself.
what are some limitations with the JC69 model in comparison to real life?
in this model all sites in the sequence evolve at the same rate but substitution rates might differ across the genome, as : 1- mutation rates might differ across sites
2- selective pressure might be different on the phenotypic level
How do we overcome the limitation on varying genome rates across sites?
by replacing the constant rated by random variables which are tau distributed with mean on 1
Ignoring site variation leads to ——-?
underestimation of the sequence distance
Are all phylogenetic reconstruction methods based on distances?
No
Can we use the same Markov model used for amino acid substitutions? if yes, are there any adjustments we should make?
yes, the substitution matrix and transitional matrix would both have dimensions of 20 x 20.
What are two types of methods for amino acid substitutions?
empiric, where we try to estimate from sequences rates and mechanistic, where we use a model framework .
For amino acid substitution, do we prefer methods with time reversiblility or not?
yes.
if we have 20 AA, what its the substitution rate for any substitution?
19 lamba
what is the expected time until a substation happens in 20 AA?
1/19lamba
To estimate the distance with an empirical or mechanistic Q matrix we use —?
MLE
We have — possible combination of nucleotides with — amino acids. M eaning —
64, 20. different combinations of nucleotides encode for the same amino acid
In a codon sun, what’s important to note?
where a gene starts and where it ends.
What are synonymous substitutions?
A substitution at which the amino acid doesn’t change e.g TTA and CTT, which still encode for CTA
What are nonsynanomous substitutions?
A substituion at which the amino acid does change.
Why do knowing whether transversion or transition occurs is important?
It is important because it gives an idea of evolutionary trajectories and evolutionary pressure.
What do we incorporate in the basic model of codon substitution?
k: transition/transversion rate ratio, w: nonsynonymous/ synonymous rate ratio, pi: equilibrium frequency of codon I consisting of nucleotides i1,i2,i3, with equilibrium requesting of each, where pi_I = 1/C*multiplicaiton of the equilibrium frequencies of each nucleotide.
synonymous substitutions do/dont? change the protein, thus they are seen as —-?
dont, neutral
