This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “The Maximum Likelihood Approach”.
1. Which of the following is wrong statement about the maximum likelihood approach?
a) This method doesn’t always involve probability calculations
b) It finds a tree that best accounts for the variation in a set of sequences
c) The method is similar to the maximum parsimony method
d) The analysis is performed on each column of a multiple sequence alignment
Explanation: This method involve probability calculations to find a tree that best accounts for the variation in a set of sequences. All possible trees are considered. Hence, the method is only feasible for a small number of sequences.
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.
Explanation: Because the rate of appearance of new mutations is very small, the more mutations needed to fit a tree to the data, the less likely that tree (Felsenstein 1981). The maximum likelihood method resembles the maximum parsimony method in that trees with the least number of changes will be the most likely.
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.
Explanation: The maximum likelihood method presents an additional opportunity to evaluate trees with variations in mutation rates in different lineages. Also it provides opportunity to use explicit evolutionary models such as the Jukes-Cantor and Kimura models with allowances for variations in base composition.
4. The main disadvantage of maximum likelihood methods is that they are _____
a) mathematically less folded
b) mathematically less complex
c) computationally lucid
d) computationally intense
Explanation: The main disadvantage of maximum likelihood methods is that they are computationally intense. However, with faster computers, the maximum likelihood method is seeing wider use and is being used for more complex models of evolution.
5. Maximum likelihood has also been used for an analysis of mutations in overlapping reading frames in viruses.
Explanation: PAUP version 4 can be used to perform a maximum likelihood analysis on DNA sequences. The method has also been applied for changes from one amino acid to another in protein sequences.
6. Which of the following is wrong statement about DNAML and DNAMLK?
a) PHYLIP includes mentioned two programs for this maximum likelihood analysis
b) DNAML estimates phylogenies from nucleotide sequences by the maximum likelihood method
c) DNAMLK estimates phylogenies in the same manner as DNAML
d) DNAMLK estimates phylogenies without molecular clock
Explanation: DNAMLK estimates phylogenies from nucleotide sequences by the maximum likelihood method in the same manner as DNAML, but assumes a molecular clock. DNAML allows for variable frequencies of the four nucleotides, for unequal rates of transitions and transversions, and for different rates of change in different categories of sites, as specified by the program.
7. Which of the following is wrong statement about the maximum likelihood method’s steps?
a) It starts with an evolutionary model of sequence change that provides estimates of rates of substitution of one base for another
b) 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
c) The rates of all possible substitutions are chosen so that the base composition differs
d) The set of sequences is then aligned
Explanation: The rates of all possible substitutions are chosen so that the base composition remains the same. The set of sequences is then aligned, and the substitutions in each column are examined for their fit to a set of trees that describe possible phylogenetic relationships among the sequences.
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.
Explanation: Because these likelihoods are very small numbers, their logarithms are usually added to give the logarithm likelihood of each tree. The most likely tree given the data is then identified.
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?
a) The basis of this method is to devise a scheme for introducing substitutions, insertions, and gaps into sequences
b) The basis of this method is to provide a probability that each of these changes occurs over certain periods of evolutionary time
c) Given each of these predicted changes, the method examines all the possible combinations of mutations to change one sequence into another
d) Multiple combinations are selected that will be the most likely over time
Explanation: One of these combinations will be the most likely one over time and that is selected. Once this combination has been determined, a sequence alignment and the distance between the sequences will be known.
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?
a) This method is different from the Smith-Waterman local alignment algorithm
b) This method is quite similar to the Smith-Waterman local alignment algorithm
c) The underlying mutational theory is like those used to produce the PAM matrices for predicting changes in DNA and protein sequences
d) 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
Explanation: This method is different from the Smith-Waterman local alignment algorithm in identifying the most probable (maximum likelihood probability alignment) based on an evolutionary model of change in sequences, as opposed to a score based on observed substitutions in related proteins and a gap scoring system. An example for option d can be–a given nucleotide at any sequence position can mutate into another at the same rate or may not change at all during a period of evolutionary time.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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