This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Maximum Parsimony Method”.
1. Which of the following is untrue regarding the maximum parsimony method?
a) This method predicts the evolutionary tree
b) It minimizes the number of steps required to generate the observed variation in the sequences
c) The method is also sometimes referred to as the minimum evolution method
d) Only a pairwise sequence alignment is required to predict which sequence positions are likely to correspond
View Answer
Explanation: A multiple sequence alignment is required to predict which sequence positions are likely to correspond. These positions will appear in vertical columns in the multiple sequence alignment. For each aligned position, phylogenetic trees that require the smallest number of evolutionary changes to produce the observed sequence changes are identified.
2. Which of the following is untrue regarding the maximum parsimony method?
a) The analysis steps are continued for every position in the sequence alignment
b) This method is used for large numbers of sequences
c) Those trees that produce the smallest number of changes overall for all sequence positions are identified
d) This method is used for sequences that are quite similar
View Answer
Explanation: The algorithm followed is not particularly complicated, but it is guaranteed to find the best tree, because all possible trees relating a group of sequences are examined. For this reason, the method is quite time-consuming and is not useful for data that include a large number of sequences or sequences with a large amount of variation.
3. Which of the following is untrue regarding the programs for analysis of nucleic acid sequences?
a) DNAPARS treats gaps as a fifth nucleotide state
b) DNAPENNY performs parsimonious phylogenies by branch-and-bound search
c) DNAPENNY can analyze sequences up to 11 or 12
d) Compatibility criterion is not involved in DNACOMP
View Answer
Explanation: DNACOMP performs phylogenetic analysis using the compatibility criterion.
Rather than searching for overall parsimony at all sites in the multiple sequence alignment, this method finds the tree that supports the largest number of sites. This method is recommended when the rate of evolution varies among sites.
4. PROTPARS counts the minimum number of mutations to change a codon for the first amino acid into a codon for the second amino acid, but only scores those mutations in the mutational path that actually change the amino acid.
a) True
b) False
View Answer
Explanation: PROTPARS is used For analysis of protein sequences. As mentioned, Silent mutations that do not change the amino acid are not scored on the grounds that they have little evolutionary significance.
5. Parsimony can give ________ information when rates of sequence change _______ in the different branches of a tree that are represented by the sequence data.
a) misleading, vary
b) useful, change
c) misleading, are constant
d) sometimes contradicting, are constant
View Answer
Explanation: These variations produce a range of branch lengths, long ones representing more extended periods of time and short ones representing shorter times. Although other columns in the sequence alignment that show less variation may provide the correct tree, the columns representing greater variation dominate the analysis.
6. Which of the following is untrue regarding the distance methods?
a) The sequence pairs that have the largest number of sequence changes between them are termed ‘neighbors’
b) On a tree, these sequences share a node or common ancestor position and are each joined to that node by a branch
c) It produces a phylogenetic tree of the group
d) It employs the number of changes between each pair in a group of sequences
View Answer
Explanation: The goal of distance methods is to identify a tree that positions the neighbors correctly and that also has branch lengths which reproduce the original data as closely as possible. Finding the closest neighbors among a group of sequences by the distance method is often the first step in producing a multiple sequence alignment.
7. Which of the following is untrue regarding the distance methods?
a) The distance method was pioneered by Feng and Doolittle
b) A collection of programs by authors Feng and Doolittle will produce both an alignment and tree of a set of protein sequences
c) The program CLUSTALW uses the neighbor-joining distance method as a guide to multiple sequence alignments
d) Among the Programs of the PHYLIP package, DNADIST is not one of them
View Answer
Explanation: DNADIST and PROTDIST are the Programs of the PHYLIP package that perform a distance analysis. They automatically read in a sequence in the PHYLIP in file format and automatically produce a file called outfile with a distance table.
8. Which of the following is untrue regarding the Distance analysis programs in PHYLIP?
a) FITCH estimates a phylogenetic tree assuming additivity of branch lengths
b) FITCH uses the Fitch-Margoliash method
c) FITCH assumes a molecular clock but KITSCH does not
d) NEIGHBOR estimates phylogenies using the neighbor-joining or unweighted pair group method with arithmetic mean (UPGMA)
View Answer
Explanation: KITSCH assumes a molecular clock but FITCH does not. Also, in NEIGHBOR the neighbor-joining method does not assume a molecular clock and produces an unrooted tree. The UPGMA method assumes a molecular clock and produces a rooted tree.
9. Which of the following is untrue regarding the neighbor-joining method?
a) It is very much like the Fitch-Margoliash method
b) It is totally dissimilar than the Fitch-Margoliash method
c) It is especially suitable when the rate of evolution of the separate lineages under consideration varies
d) When the branch lengths of trees of known topology are allowed to vary in a manner that simulates varying levels of evolutionary change, it is the most reliable method
View Answer
Explanation: The neighbor-joining method is very much like the Fitch-Margoliash method except that the choice as to which sequences to pair is determined by a different algorithm. In the situation mentioned in option d, the neighbor-joining method and the Sattath and Taversky method, are the most reliable in predicting the correct tree.
10. Neighbor-joining chooses the sequences that should be joined to give the best least squares estimates of the branch lengths that most closely reflect the actual distances between the sequences.
a) True
b) False
View Answer
Explanation: It is not necessary to compare all possible trees to find the least squares fit as in the Fitch-Margoliash method. The method pairs sequences based on the effect of the pairing on the sum of the branch lengths of the tree.
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