# Bioinformatics Questions and Answers – Methods

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This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Methods”.

1. The overall goal of pair wise sequence alignment is to find the best pairing of two sequences, such that there is maximum correspondence among residues.
a) True
b) False

Explanation: The goal of pair wise sequence alignment is to find the best pairing and to achieve this goal; one sequence needs to be shifted relative to the other to find the position where maximum matches are found. There are two different alignment strategies that are often used: global alignment and local alignment.

2. In local alignment, the two sequences to be aligned cannot be of unequal lengths.
a) True
b) False

Explanation: The two sequences to be aligned can be of different lengths. This approach is more appropriate for aligning divergent biological sequences containing only modules that are similar, which are referred to as domains or motifs. This approach can be used for aligning more divergent sequences with the goal of searching for conserved patterns in DNA or protein sequences.

3. Alignment algorithms, both global and local, are fundamentally similar and only differ in the optimization strategy used in aligning similar residues.
a) True
b) False

Explanation: Both types of algorithms can be based on one of the three methods: the dot matrix method, the dynamic programming method, and the word method. The word method is used in fast database similarity searching.

4. In a dot matrix, two sequences to be compared are written in the _____________ of the matrix.
a) horizontal and vertical axes
b) 2 parallel horizontal axes
c) 2 parallel vertical axes
d) horizontal axis (one preceding another)

Explanation: The comparison is done by scanning each residue of one sequence for similarity with all residues in the other sequence. If a residue match is found, a dot is placed within the graph. Otherwise, the matrix positions are left blank.

5. When the two sequences have substantial regions of similarity, many dots line up to form contiguous _______ lines.
a) crossings on
b) horizontal
c) diagonal
d) vertical

Explanation: The dots line up to form contiguous diagonal lines, which reveal the sequence alignment. If there are interruptions in the middle of a diagonal line, they indicate insertions or deletions. Parallel diagonal lines within the matrix represent repetitive regions of the sequences.

6. A problem exists when comparing _____ sequences using the dot matrix method, namely, the _______
a) small, amplification
b) large, amplification
c) small, high noise level
d) large, high noise level

Explanation: In most dot plots, dots are plotted all over the graph obscuring identification of the true alignment. For DNA sequences, the problem is particularly acute because there are only four possible characters in DNA and each residue therefore has a one-in-four chance of matching a residue in another sequence.

7. If the selected window size is too long, sensitivity of the alignment is lost.
a) True
b) False

Explanation: Dots are only placed when a stretch of residues equal to the window size from one sequence matches completely with a stretch of another sequence. This method has been shown to be effective in reducing the noise level. The window is also called a tuple, the size of which can be manipulated so that a clear pattern of sequence match can be plotted. However, if the selected window size is too long, sensitivity of the alignment is lost.

8. A sequence can be aligned with itself to identify internal repeat elements.
a) True
b) False

Explanation: In the self comparison, there is a main diagonal for perfect matching of each residue. If repeats are present, short parallel lines are observed above and below the main diagonal.

9. Self complementarity of DNA sequences cannot be identified using a dot plot.
a) True
b) False

Explanation: Self complementarity of DNA sequences, also called inverted repeats can be identified using a dot plot. For example, those that forms the stems of a hairpin structure. In this case, a DNA sequence is compared with its reverse-complemented sequence. Parallel diagonals represent the inverted repeats.

10. Which of the following is untrue about dot plot method and its applications?
a) This method gives a direct visual statement of the relationship between two sequences
b) One of its advantages is the identification of sequence repeat regions based on the presence of parallel diagonals of the same size vertically or horizontally in the matrix
c) It is not useful in identifying chromosomal repeats
d) The method can be used in identifying nucleic acid secondary structures through detecting self-complementarity of a sequence 