Which of the following is not true about iterative methods?

Genetic Algorithm is method used for under this

Hidden Markov Models are used for Multiple Sequence Alignment

The objective is to improve the overall alignment score

MultAlin recalculates global scores

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

To study evolutionary relationships

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

Which of the following is not a feature of editors and formatters?

provision for displaying the sequence on a color monitor with residue colors to aid in a clear visual representation of the alignment

recognition of the multiple sequence format that was output by the MSA (Multiple Sequence Alignment) program

maintenance of the alignment in a suitable format when the editing is completed

disallowing shading conserved residues in the alignment

Which of the following is untrue regarding the progressive alignment method?

The program also applies a weighting scheme to increase the reliability of aligning divergent sequences (sequences with less than 25% identity)

The progress is done by down weighting redundant and closely related groups of sequences in the alignment by a certain factor

This scheme is useful in enhancing similar sequences from dominating the alignment

Which of the following is not a drawback of the progressive alignment method?

The final alignment result is also influenced by the order of sequence addition

The progressive alignment method is not suitable for comparing sequences of different lengths because it is a global alignment–based method

In this method the use of affine gap penalties, long gaps are not allowed, and, in some cases, this may limit the accuracy of the method

In this method the use of affine gap penalties, long gaps is allowed, and, in some cases, this may limit the accuracy of the method

The final alignment result is also influenced by the order of sequence addition

The quality and quantity of information provided by the PSSM also varies for ________ in the motif.

neither the rows nor the columns

Two considerations arise in trying to tune the PSSM so that it adequately represents the training sequences. Which of the following is not their description?

If the number of sequences with the found motif is large and reasonably diverse, the sequences represent a good statistical sampling of all sequences that are ever likely to be found with that same motif

If a given column in 20 sequences has only isoleucine, it is not very likely that different amino acid will be found in other sequences with that motif because the residue is probably important for function

If a given column in 20 sequences has only isoleucine, it is very likely that different amino acid will be found in other sequences with that motif because the residue is probably important for function

If the number of sequences with the found motif is large and reasonably diverse, the sequences represent a good statistical sampling of all sequences that are ever likely to be found with that same motif

Another column in the motif from the 20 sequences may have several amino acids, and some amino acids may not be represented at all

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 also an essential prerequisite to carrying out phylogenetic analysis of sequence families and prediction of protein secondary and tertiary 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

78 + Mcqs in Multiple Sequence Alignment in Bioinformatics Page 2 McqOptions

51.	Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

53.	The first step in Genetic Algorithm is arranging the sequences to be aligned in rows.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

54.	For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.
A.	30
B.	21
C.	81
D.	60
Answer» D. 60

55.	The second step in the Genetic Algorithm comprises of scoring of the 100 initial MSAs by the sum of pairs method.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

56.	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
C.	May be True or False
D.	Can't say
Answer» B. False

57.	If the data set is _______ then unless the motif has __________ amino acids in each column, the column frequencies in the motif may not be highly representative of all other occurrences of the motif.
A.	small, distinct
B.	small, almost identical
C.	large, almost identical
D.	large, distinct
Answer» C. large, almost identical

58.	In a multidimensional search matrix, for aligning N sequences, an (N+2)-dimensional matrix is needed to be filled with alignment scores.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

59.	A dotplot is a visual and qualitative technique whereas the sequence alignment is an exact and quantitative measure of similarity of alignments.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

60.	The Genetic Algorithm method has been recently adapted for MSA(Multiple Sequence Alignment) by Corpet (1998).
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

61.	In the program DIALIGN, pairs of sequences are aligned to locate aligned regions that do not include gaps, much like continuous diagonals in a dot matrix plot.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

62.	In the intermediate steps of EM algorithm, the number of each base in each column is determined and then converted to fractions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

74.	Which of the following scores are not considered while calculating the SP scores?
A.	All possible pair wise matches
B.	All possible mismatches
C.	All possible gap costs
D.	Number of gap penalties
Answer» E.

66.	In the method of extraction of blocks from a global or local MSA, a global MSA of related protein sequences usually includes regions that have been aligned without gaps in any of the sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

68.	MACAW is a local multiple sequence alignment program only.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

69.	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
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

70.	In Genetic Algorithm, in the mutation process _______
A.	sequence is changed
B.	gaps are not inserted
C.	sequence is not changed
D.	gaps are not rearranged
Answer» D. gaps are not rearranged

71.	The quality and quantity of information provided by the PSSM also varies for ________ in the motif.
A.	each row
B.	each column
C.	rows and columns
D.	neither the rows nor the columns
Answer» C. rows and columns

72.	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
C.	May be True or False
D.	Can't say
Answer» B. False

75.	There is a unique advantage of multiple sequence alignment because it reveals more biological information than many pair wise alignments can.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

76.	Related sequences are identified through the database similarity searching and as the process generates multiple matching sequence pairs, it is often necessary to convert the numerous pair wise alignments into a single alignment.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

77.	The scoring function for multiple sequence alignment is based on the concept of sum of pairs (SP).
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Even if many pseudocounts are added in comparison to real sequence counts, the amino acid frequencies will not have any effect or influence.

Which of the following is not true about iterative methods?

The first step in Genetic Algorithm is arranging the sequences to be aligned in rows.

For the 10-residue DNA sequence example, there are _______ possible starting sites for a 20-residue-long site.

The second step in the Genetic Algorithm comprises of scoring of the 100 initial MSAs by the sum of pairs method.

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.

If the data set is _______ then unless the motif has __________ amino acids in each column, the column frequencies in the motif may not be highly representative of all other occurrences of the motif.

In a multidimensional search matrix, for aligning N sequences, an (N+2)-dimensional matrix is needed to be filled with alignment scores.

A dotplot is a visual and qualitative technique whereas the sequence alignment is an exact and quantitative measure of similarity of alignments.

The Genetic Algorithm method has been recently adapted for MSA(Multiple Sequence Alignment) by Corpet (1998).

In the program DIALIGN, pairs of sequences are aligned to locate aligned regions that do not include gaps, much like continuous diagonals in a dot matrix plot.

In the intermediate steps of EM algorithm, the number of each base in each column is determined and then converted to fractions.

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

Which of the following is not a feature of editors and formatters?

Which of the following is untrue regarding the progressive alignment method?

In the method of extraction of blocks from a global or local MSA, a global MSA of related protein sequences usually includes regions that have been aligned without gaps in any of the sequences.

Which of the following is not a drawback of the progressive alignment method?

MACAW is a local multiple sequence alignment program only.

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.

In Genetic Algorithm, in the mutation process _______

The quality and quantity of information provided by the PSSM also varies for ________ in the motif.

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.

Two considerations arise in trying to tune the PSSM so that it adequately represents the training sequences. Which of the following is not their description?

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

There is a unique advantage of multiple sequence alignment because it reveals more biological information than many pair wise alignments can.

Related sequences are identified through the database similarity searching and as the process generates multiple matching sequence pairs, it is often necessary to convert the numerous pair wise alignments into a single alignment.

The scoring function for multiple sequence alignment is based on the concept of sum of pairs (SP).

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

If the data set is _ then unless the motif has ____ amino acids in each column, the column frequencies in the motif may not be highly representative of all other occurrences of the motif.