gs gs120 Statistical Inference and Regression Models - Likelihood - Quiz No.1

gs gs120 Data Structure Quiz

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Question 1: Which of the following is wrong statement about the maximum likelihood approach?

This method doesn’t always involve probability calculations

It finds a tree that best accounts for the variation in a set of sequences

The method is similar to the maximum parsimony method

The analysis is performed on each column of a multiple sequence alignment

Question 2: In about the maximum likelihood approach, for each tree, the number of sequence changes or mutations that may have occurred to give the sequence variation is considered.

True

False

Question 3: The maximum likelihood method can be used to explore relationships among more diverse sequences, conditions that are not well handled by maximum parsimony methods.

True

False

Question 4: The main disadvantage of maximum likelihood methods is that they are _____

mathematically less folded

mathematically less complex

computationally lucid

computationally intense

Question 5: Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.

True

False

Question 6: Which of the following is wrong statement about DNAML and DNAMLK?

PHYLIP includes mentioned two programs for this maximum likelihood analysis

DNAML estimates phylogenies from nucleotide sequences by the maximum likelihood method

DNAMLK estimates phylogenies in the same manner as DNAML

DNAMLK estimates phylogenies without molecular clock

Question 7: Which of the following is wrong statement about the maximum likelihood method’s steps?

It starts with an evolutionary model of sequence change that provides estimates of rates of substitution of one base for another

In the beginning there is an evolutionary model of sequence change that provides estimates of transitions and transversions in a set of nucleic acid sequences

The rates of all possible substitutions are chosen so that the base composition differs

The set of sequences is then aligned

Question 8: Once all positions in the sequence alignment have been examined, the likelihoods given by each column in the alignment for each tree are _____ to give the likelihood of the tree.

multiplied

added

divided

squared

Question 9: A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

The basis of this method is to devise a scheme for introducing substitutions, insertions, and gaps into sequences

The basis of this method is to provide a probability that each of these changes occurs over certain periods of evolutionary time

Given each of these predicted changes, the method examines all the possible combinations of mutations to change one sequence into another

Multiple combinations are selected that will be the most likely over time

Question 10: A method of sequence alignment based on a Model (Bishop and Thompson 1986) was introduced that predicts the manner in which DNA sequences change during evolution. Which of the following is wrong about it?

This method is different from the Smith-Waterman local alignment algorithm

This method is quite similar to the Smith-Waterman local alignment algorithm

The underlying mutational theory is like those used to produce the PAM matrices for predicting changes in DNA and protein sequences

Sequences are predicted to change by a Markov process such that each mutation in the sequence is independent of previous mutations at that site or at other sites