The Progressive and Iterative Methods of Multiple Sequence Alignment

This quiz contains multiple-choice problems on exhaustive and heuristic algorithms, Needleman-Wunsch algorithm, progressive and iterative methods of multiple sequence alignment, sequences localized alignment, alignment aiding statistical methods and specific scoring matrices.

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Related sequences are identified through database similarity searching. As the process generates multiple matching sequence pairs, converting the numerous pairwise alignments into a single alignment is often necessary. True or false?

True

False

Multiple sequence alignment has a unique advantage because it reveals more biological information than many pairwise alignments can. True or false?

True

False

Which of the following cannot be related to multiple sequence alignment?

Many conserved and functionally critical amino acid residues can be identified in a protein multiple alignment

Multiple sequence alignment is an essential prerequisite to carrying out the phylogenetic analysis of sequence families and prediction of secondary and tertiary protein structures

Multiple sequence alignment also has applications in designing degenerate polymerase chain reaction (PCR) primers based on multiple related sequences

This method does not contribute much to degenerate polymerase chain reaction (PCR) primers creation

The scoring function for multiple sequence alignment is based on the ‘sum-of-pairs’ concept. True or false?

True

False

Which of the following are not considered whilst calculating the SP scores?

All possible pair wise matches

All possible mismatches

All possible gap costs

Number of gap penalties

There are two approaches, viz. exhaustive and heuristic, used in multiple sequence alignment. True or false?

True

False

Given the multiple alignments of three sequences, the sum of scores is calculated as that of the dissimilarity scores for every pair of sequences at each position. True or false?

True

False

An (N+2)-dimensional matrix must be filled with alignment scores for aligning N sequences in a multidimensional search matrix. True or false?

True

False

The amount of computational time and memory space required increases exponentially with the number of sequences, making the multidimensional search matrix method computationally prohibitive to use for a large data set. True or false?

True

False

Which of the following is untrue about DCA?

It stands for Divide-and-Conquer Alignment

It works by breaking each of the sequences into two smaller sections

The breaking points during the process are determined based on regional similarity of the sequences

If the sections are not short enough, further divisions are restricted as well

Which of the following is not an objective to perform sequence comparison?

To observe patterns of conservation

To find the common motifs present in both sequences

To study the physical properties of molecules

To study evolutionary relationships

The dot plot is a visual and qualitative technique, whereas the sequence alignment is an exact and quantitative measure of similarity of alignments. True or false?

True

False

Which of the following is untrue about protein substitution matrices?

They are significantly more complex than DNA scoring matrices

They have the N x N matrices of the amino acids

Protein substitution matrices have quite important role in evolutionary studies

They are significantly quite less complex than DNA scoring matrices

Which of the following is untrue about Needleman-Wunsch algorithm?

It is an example of dynamic programming

Basic idea here is to build up the best alignment by using optimal alignments of larger subsequences

It was first used by Saul Needleman and Christian Wunsch

It was first used in 1970