# Bioinformatics Questions and Answers – Progressive Methods of Multiple Sequence Alignment

This set of Bioinformatics Quiz focuses on “Progressive Methods of Multiple Sequence Alignment”.

1. Progressive alignment methods use the dynamic programming method to build an MSA starting with the most related sequences and then progressively adding less related sequences or groups of sequences to the initial alignment.
a) True
b) False

Explanation: The progressive alignment methods use the dynamic programming method. Relationships among the sequences are modeled by an evolutionary tree in which the outer branches or leaves are the sequences. The tree is based on pair-wise comparisons of the sequences using one of the phylogenetic methods.

2. Progenitor sequences represented by the ______ branches of the tree are derived by alignment of the _______ sequences.
a) outer, outermost
b) inner, outermost
c) inner, innermost
d) outer, innermost

Explanation: Progenitor sequences represented by the inner branches of the tree are derived by alignment of the outermost sequences. These inner branches will have uncertainties where positions in the outermost sequences are dissimilar.

3. CLUSTALW is a more recent version of CLUSTAL with the W standing for ________
a) weakening
b) winding
c) weighting
d) wiping

Explanation: The W in CLUSTALW stands for ‘weighting’ to represent the ability of the program to provide weights to the sequence and program parameters. CLUSTAL has been around for more than 10 years and lots of improvements in the program have been made.

4. The CLUSTALX provides a graphic interface.
a) True
b) False

Explanation: Two examples of programs that use progressive methods are CLUSTALW and the Genetics Computer Group program PILEUP. CLUSTALX provides a graphic interface.
These changes provide more realistic alignments that should reflect the evolutionary changes in the aligned sequences and the more appropriate distribution of gaps between conserved domains.

5. Which of the following is untrue about CLUSTAL program?
a) CLUSTAL performs a global-multiple sequence alignment by a different method than MSA (Multiple Sequence Alignment)
b) The initial heuristic alignment obtained by MSA is calculated in a different way
c) The initial step includes performing pair-wise alignments of all of the sequences
d) The intermediate step includes use the alignment scores to produce a phylogenetic tree

Explanation: The initial heuristic alignment obtained by MSA is calculated the same way, although it performs a global-multiple sequence alignment by a different method than MSA (Multiple Sequence Alignment). As the mentioned options are first two steps, the last is aligning the sequences sequentially, guided by the phylogenetic relationships indicated by the tree.
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6. The initial alignments used to produce the guide tree may be obtained by various methods. Which of the following is not one of them?
a) Fast k-tuple
b) pattern-finding approach similar
c) FASTA
d) Faster, full dynamic programming method

Explanation: The methods used, might be fast k-tuple or pattern-finding approach similar to FASTA that is useful for many sequences and the full dynamic programming method as well. But the option d becomes incorrect as full dynamic programming method is slower as compared to rest of the methods in options.

7. The scoring of gaps in a MSA (Multiple Sequence Alignment) has to be performed in a different manner from scoring gaps in a pair-wise alignment.
a) True
b) False

Explanation: As more sequences are added to a profile of an existing MSA, gaps accumulate and influence the alignment of further sequences. CLUSTALW calculates gaps in a novel way designed to place them between conserved domains.

8. Like other alignment programs, CLUSTAL uses a null score for opening a gap in a sequence alignment and a penalty for extending the gap by one residue.
a) True
b) False

Explanation: CLUSTAL uses a penalty for opening a gap in a sequence alignment and an additional penalty for extending the gap by one residue. These penalties are user-defined. Gaps found in the initial alignments remain fixed. New gaps introduced as more sequences are added also receive this same gap penalty, even when they occur within an existing gap, but the gap penalties for alignment are then modified according to the average match value in the substitution matrix, the percent identity between the sequences, and the sequence lengths.

9. Which of the following is untrue about PILEUP program?
a) It is the MSA program that is a part of the Genetics Computer Group package of sequence analysis programs
b) It is owned since 1997 by Oxford Communications and is widely used due to the popularity and availability of this package
c) It uses a method for MSA that is polar opposite to CLUSTALW
d) The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm

Explanation: PILEUP uses a method for MSA that is very similar to CLUSTALW. The sequences are aligned pair-wise using the Needleman- Wunsch dynamic programming algorithm, and the scores are used to produce a tree by the unweighted pair-group method using arithmetic averages. The resulting tree is then used to guide the alignment of the most closely related sequences and groups of sequences. The resulting alignment is a global alignment produced by the Needleman-Wunsch algorithm.

10. The resulting tree is then used to guide the alignment of the most closely related sequences and groups of sequences. The resulting alignment is a global alignment produced by the Needleman-Wunsch algorithm.
a) True
b) False

Explanation: The very first sequences to be aligned are the most closely related on the sequence tree. If these sequences align very well, there will be few errors in the initial alignments. However, the more distantly related these sequences, the more errors will be made, and these errors will be propagated to the MSA. There is no simple way to circumvent this problem. A second problem with the progressive alignment method is the choice of suitable scoring matrices and gap penalties that apply to the set of sequences.

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