Bioinformatics MCQs Part 14

1. A bifurcating branch point in the phylogenetic tree is known as ______.

• Node
• Clade
• Branch
• Taxon

2. Bootstrapping repeats the phylogenetic analysis several times, each time reshuffling the columns of the initial alignment, in order to _______.

• build a consensus tree, where the number of times each branch reforms is counted and used to estimate its probability.
• Generate a random model from which to benchmark phylogenetic data.
• Produce a graphical representation of the tree.
• Assess the probability that the sequences in the alignment are unrelated.

3. Expand UPGMA.

• Unweighted Pair Group Method with Arithmetic Mean.
• Unweighted Pair Group Method with All Mean.
• Upregulated Gene Method with Arithmetic Mean.
• Unregulated Genome Method with All Mean.

4. Single substitution in the nucleotide sequence is called ________.

• Single substitution.
• Simple substitution.
• Single nucleotide polymorphism.
• Simple nucleotide polymorphism.

5. Which one of the following is more weighted mutation?

• Transition
• Transversions
• Transitions and transversion
• Deletion

6. One of the most common errors in making and analyzing phylogenetic tree is ________.

• Using a bad multiple sequence alignment as input
• Trying to infer the evolutionary relationship of genes or proteins in the tree
• Trying to infer the age at which genes or proteins diverged from each other
• Assuming that clades are monophyletic

7. Which one of the following tool can be used to generate neighbour joining trees with or without bootstrap values?

• ClustalX
• BLASt
• Swiss-PDB viewer
• ChemSketch

8. If you have 200 viral DNA sequences of 500 residues each and you want to know if there are any pairs that are identical or nearly identical. Which of the following is the most efficient method to use?

• BLASt
• Maximum-likelihood phylogenetic analysis
• Neighbour-joining phylogenetic analysis
• PopSet

9. Which one of the following tools can be used for both modeling the protein and structure visualization?

• Swiss-PDB Viewer
• QMol
• RasMol
• ChemSketch

10. Homololgy modeling can be done using _____.

• Swiss-PDB Viewer
• QMol
• Raswin
• Babel

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