This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Reliability of Phylogenetic Predictions”.
1. Phylogenetic analysis of a set of sequences that aligns ______ is straightforward because the positions that correspond in the sequences can be readily identified in a ______ of the sequences.
a) very well, multiple sequence alignment
b) in a haphazard manner, multiple sequence alignment
c) in a distorted way, multiple sequence alignment
d) very well, self alignment
Explanation: Option d, here, becomes irrelevant as there is phylogenetic analysis involved. The types of changes in the aligned positions or the numbers of changes in the alignments between pairs of sequences then provide a basis for a determination of phylogenetic relationships among the sequences by the above methods of phylogenetic analysis.
2. For sequences that have ______, a phylogenetic analysis is_______
a) diverged considerably, more challenging
b) not diverged, more challenging
c) diverged considerably, less challenging
d) diverged considerably, a less work to do
Explanation: Clearly, option a and b contradict. For diverged sequences, the analysis steps increase as well. A determination of the sequence changes that have occurred is more difficult because the multiple sequence alignment may not be optimal and because multiple changes may have occurred in the aligned sequence positions.
3. The choice of a suitable multiple sequence alignment method depends on the degree of variation among the sequences.
Explanation: The degree of variation also sometimes affecs the efficiency and nature of output. Once a suitable alignment has been found, one may also ask how well the predicted phylogenetic relationships are supported by the data in the multiple sequence alignment.
4. In the bootstrap method, the data are resampled by _____ choosing _____ columns from the aligned sequences to produce, in effect, a new sequence alignment of the_____
a) randomly, horizontal, same length
b) specifically, vertical, different lengths
c) randomly, vertical, same length
d) randomly, vertical, different lengths
Explanation: Each column of data may be used more than once and some columns may not be used at all in the new alignment. Trees are then predicted from many of these alignments of resampled sequences (Felsenstein 1988).
5. In the bootstrap method, for branches in the predicted tree topology to be significant, the resampled data sets should frequently predict the same branches.
Explanation: Bootstrap analysis is supported by most of the commonly used phylogenetic inference software packages and is commonly used to test tree branch reliability. Another method of testing the reliability of one part of the tree is to collapse two branches into a common node (Maddison and Maddison 1992).
6. In the final steps of the bootstrap method, the _____ the decay value, the ___ significant the original branches.
a) greater, less
b) greater, more
c) lesser, more
d) more, less
Explanation: In the final steps of the bootstrap method,The tree length is again evaluated and compared to the original length, and any increase is the decay value. The greater the decay value, the more significant the original branches. In addition to these methods, there are some additional recommendations that increase confidence in a phylogenetic prediction.
7. A common recommendation is to use at least two of the methods—maximum parsimony, distance, or maximum likelihood, for the analysis.
Explanation: If two of these methods provide the same prediction, confidence in the prediction is much higher. Another recommendation is to pay careful attention to the evolutionary assumptions and models that are used for both sequence alignment and tree construction.
8. The traditional use of phylogenetic analysis is to discover evolutionary relationships among species.
Explanation: In such cases, a suitable gene or DNA sequence that shows just enough, but not too much, variation among a group of organisms is selected for phylogenetic analysis. For example, analysis of mitochondrial sequences is used to discover evolutionary relationships among mammals.
9. Two more recent uses of phylogenetic analysis are to analyze ______ and to trace the evolutionary history of specific genes. Which of the following could not be the correct blank?
a) gene families
d) physical separation methods
Explanation: Option, here, indicates the laboratory operations unlike the computational data mentioned in other options. For example, database similarity searches may identify several proteins in a plant genome that are similar to a yeast query protein.
10. Tracking the evolutionary history of individual genes in a group of species can reveal which genes have remained in a genome for a long time and which genes have been horizontally transferred between species.
Explanation: Thus, phylogenetic analysis can also contribute to an understanding of genome evolution. Or e.g. from a phylogenetic analysis of the protein family, the plant gene most closely related to the yeast gene and therefore most likely to have the same function can be determined.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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