Which of the following is not correct about FASTA?

It was in fact the first database similarity search tool developed, preceding the development of BLAST

FASTA uses a ‘hashing’ strategy to find matches for a short stretch of identical residues with a length of k

The string of residues is known as blocks

BLAST uses a _______ to find matching words, whereas FASTA identifies identical matching words using the _____

substitution matrix, hashing procedure

hashing procedure, substitution matrix

Which of the following is not a benefit or a factual of FASTA over BLAST?

It gives results with a better coverage rate for homologs

FASTA scans smaller window sizes

It gives more sensitive results

It gives less sensitive results

It gives results with a better coverage rate for homologs

Which of the following is not correct about BLAST?

The BLAST web server has been designed in such away as to simplify the task of program selection

The programs are organized based on the type of query sequences

The programs are organized based on the type of nucleotide sequences, or nucleotide sequence to be translated

BLAST is not based on heuristic searching methods

Which of the following is incorrect the ‘word’ method?

Both BLAST and FASTA use a heuristic word method

Word method is used for fast pairwise sequence alignment in BLAST and FASTA

The basic assumption is that two related sequences must have at least one word in common

Two related sequences must have at zero word in common while assuming

49 + Mcqs in Database Similarity Searching in Bioinformatics Page 1 McqOptions

1.	Which of the following is not a variant of BLAST?
A.	BLASTN
B.	BLASTP
C.	BLASTX
D.	TBLASTNX
Answer» E.

Discussion

2.	Z-score describes the number of standard deviations from the mean score for the database search.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

3.	Which of the following is not a benefit of BLAST?
A.	Handling of gaps
B.	Speed
C.	More sensitive
D.	Statistical rigor
Answer» B. Speed

Discussion

4.	Scan PS is a web-based program that implements a modified version of the Needleman-Wunsch algorithm.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

5.	BLASTX uses protein sequences as queries to search against a protein sequence database.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

6.	The positional difference for each word between the two sequences is obtained by ________ the position of the ______ sequence from that of the _______ sequence and is expressed as the offset.
A.	subtracting, second, first
B.	adding, second, first
C.	adding, first, second
D.	subtracting, first, second
Answer» E.

Discussion

7.	BLAST might not find matches for very short sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

8.	The second step in FASTA is to narrow down the high similarity regions between the two sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

9.	Par Align is a web-based server that uses parallel processors to perform exhaustive sequence comparisons using either a parallelized version of the Smith–Waterman algorithm or a heuristic program for further speed gains.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

10.	Which of the following is not correct about FASTA?
A.	Its stands for FAST ALL
B.	It was in fact the first database similarity search tool developed, preceding the development of BLAST
C.	FASTA uses a ‘hashing’ strategy to find matches for a short stretch of identical residues with a length of k
D.	The string of residues is known as blocks
Answer» E.

Discussion

11.	In FASTA, For a Z-score > 15, the match can be considered extremely ______ with _____ of a homologous relationship.
A.	insignificant, uncertainty
B.	significant, uncertainty
C.	significant, certainty
D.	insignificant, certainty
Answer» D. insignificant, certainty

Discussion

12.	In Smith–Waterman algorithm, in initialization Step, the _________ row and ________ column are subject to gap penalty.
A.	first, first
B.	first, second
C.	second, First
D.	first, last
Answer» B. first, second

Discussion

13.	The use of low-complexity masking in the BLAST procedure means that it may have higher specificity than FASTA because potential false positives are reduced.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

14.	The web-based FASTA program is offered by the European Bioinformatics Institute.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

15.	FASTA is derived from logic of the dot plot.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

16.	If one is looking for protein homologs encoded in newly sequenced genomes, one may use TBLASTN, which translates nucleotide database sequences in all six open reading frames.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

17.	The initiation of FASTA format has ____ symbol.
A.	>
B.	<
C.	/
D.	*
Answer» B. <

Discussion

18.	The gapped portion in the diagonals represents matches in FASTA.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

19.	BLAST uses a _______ to find matching words, whereas FASTA identifies identical matching words using the _____
A.	substitution matrix, hashing procedure
B.	substitution matrix, blocks
C.	hashing procedure, substitution matrix
D.	ktups, substitution matrix
Answer» B. substitution matrix, blocks

Discussion

20.	The first step in FASTA alignment id to arrange the sequences in matrices’ rows and columns in order to be analyzed.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

21.	Which of the following is not a benefit or a factual of FASTA over BLAST?
A.	FASTA scans smaller window sizes
B.	It gives more sensitive results
C.	It gives less sensitive results
D.	It gives results with a better coverage rate for homologs
Answer» D. It gives results with a better coverage rate for homologs

Discussion

22.	The last step is to perform a statistical evaluation of the final alignment as in BLAST, which produces the E-value.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

23.	In FASTA, neighboring high-scoring segments along the same diagonal are selected and joined to form a single alignment.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

24.	BLAST often produces several short HSPs rather than a single aligned region.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

25.	The rigorous dynamic programming method is normally not used for database searching because it is slow and computationally expensive.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

26.	Which of the following is not correct about BLAST?
A.	The BLAST web server has been designed in such away as to simplify the task of program selection
B.	The programs are organized based on the type of query sequences
C.	The programs are organized based on the type of nucleotide sequences, or nucleotide sequence to be translated
D.	BLAST is not based on heuristic searching methods
Answer» E.

Discussion

27.	FASTX, which compares a protein query sequence to a translated DNA database.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

28.	FASTA and BLAST are __________ but __________ for larger datasets.
A.	faster, more sensitive
B.	faster, less sensitive
C.	slower, less sensitive
D.	slower, more sensitive
Answer» C. slower, less sensitive

Discussion

29.	FASTA doesn’t use bit scores.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

30.	TBLASTX queries protein sequences to anucleotide sequence database with the sequences translated in all six reading frames.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

31.	Local sequence alignments are necessary for many cases out of which one is repeated.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

32.	Score can be negative in Smith–Waterman algorithm.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

33.	The function of the scoring matrix is to conduct one-to-one comparisons between all components in two sequences and record the optimal alignment results.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

34.	In SW algorithm, to align two sequences of lengths of m and n _________ time is required.
A.	O(mn)
B.	O(m²n)
C.	O(m²n³)
D.	O(mn²)
Answer» C. O(m²n³)

Discussion

35.	One of the challenges in SWA is obtaining correct alignments in regions of low similarity between distantly related biological sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

36.	Which of the following is incorrect the ‘word’ method?
A.	Both BLAST and FASTA use a heuristic word method
B.	Word method is used for fast pairwise sequence alignment in BLAST and FASTA
C.	The basic assumption is that two related sequences must have at least one word in common
D.	Two related sequences must have at zero word in common while assuming
Answer» E.

Discussion

37.	In heuristic methods, speed doesn’t vary with the size of database.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

38.	An increase in sensitivity is associated with _______ in selectivity.
A.	no specific change
B.	increase
C.	decrease
D.	exponential increase
Answer» D. exponential increase

Discussion

39.	Currently, there are two major heuristic algorithms for performing database searches: BLAST and FASTA.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

40.	In sequence alignment by BLAST, each word from query sequence is typically _______ residues for protein sequences and _______ residues for DNA sequences.
A.	ten, eleven
B.	three, three
C.	three, eleven
D.	three, ten
Answer» D. three, ten

Discussion

41.	In sequence alignment by BLAST, the second step is to search a sequence database for the occurrence of these words.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

42.	The BLAST program was developed in _______
A.	1992
B.	1995
C.	1990
D.	1991
Answer» D. 1991

Discussion

43.	The final step involves pairwise alignment by extending from the words in both directions while counting the alignment score using the same substitution matrix.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

44.	A recent improvement in the implementation of BLAST is the ability to provide gapped alignment.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

45.	The main application of pairwise alignment is retrieving biological sequences in databases based on similarity.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

46.	Dynamic programming method is the fastest and most practical method.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

47.	The specificity refers to the ability to include incorrect hits.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

Discussion

48.	Which of the following is not one of the requirements for implementing algorithms for sequence database searching?
A.	Size of the dataset
B.	Sensitivity
C.	Specificity
D.	Speed
Answer» B. Sensitivity

Discussion

49.	Sensitivity refers to the ability to find as many correct hits as possible.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Discussion

Explore topic-wise MCQs in Bioinformatics.

Which of the following is not a variant of BLAST?

Z-score describes the number of standard deviations from the mean score for the database search.

Which of the following is not a benefit of BLAST?

Scan PS is a web-based program that implements a modified version of the Needleman-Wunsch algorithm.

BLASTX uses protein sequences as queries to search against a protein sequence database.

The positional difference for each word between the two sequences is obtained by ________ the position of the ______ sequence from that of the _______ sequence and is expressed as the offset.

BLAST might not find matches for very short sequences.

The second step in FASTA is to narrow down the high similarity regions between the two sequences.

Par Align is a web-based server that uses parallel processors to perform exhaustive sequence comparisons using either a parallelized version of the Smith–Waterman algorithm or a heuristic program for further speed gains.

Which of the following is not correct about FASTA?

In FASTA, For a Z-score > 15, the match can be considered extremely ______ with _____ of a homologous relationship.

In Smith–Waterman algorithm, in initialization Step, the _________ row and ________ column are subject to gap penalty.

The use of low-complexity masking in the BLAST procedure means that it may have higher specificity than FASTA because potential false positives are reduced.

The web-based FASTA program is offered by the European Bioinformatics Institute.

FASTA is derived from logic of the dot plot.

If one is looking for protein homologs encoded in newly sequenced genomes, one may use TBLASTN, which translates nucleotide database sequences in all six open reading frames.

The initiation of FASTA format has ____ symbol.

The gapped portion in the diagonals represents matches in FASTA.

BLAST uses a _______ to find matching words, whereas FASTA identifies identical matching words using the _____

The first step in FASTA alignment id to arrange the sequences in matrices’ rows and columns in order to be analyzed.

Which of the following is not a benefit or a factual of FASTA over BLAST?

The last step is to perform a statistical evaluation of the final alignment as in BLAST, which produces the E-value.

In FASTA, neighboring high-scoring segments along the same diagonal are selected and joined to form a single alignment.

BLAST often produces several short HSPs rather than a single aligned region.

The rigorous dynamic programming method is normally not used for database searching because it is slow and computationally expensive.

Which of the following is not correct about BLAST?

FASTX, which compares a protein query sequence to a translated DNA database.

FASTA and BLAST are __________ but __________ for larger datasets.

FASTA doesn’t use bit scores.

TBLASTX queries protein sequences to anucleotide sequence database with the sequences translated in all six reading frames.

Local sequence alignments are necessary for many cases out of which one is repeated.

Score can be negative in Smith–Waterman algorithm.

The function of the scoring matrix is to conduct one-to-one comparisons between all components in two sequences and record the optimal alignment results.

In SW algorithm, to align two sequences of lengths of m and n _________ time is required.

One of the challenges in SWA is obtaining correct alignments in regions of low similarity between distantly related biological sequences.

Which of the following is incorrect the ‘word’ method?

In heuristic methods, speed doesn’t vary with the size of database.

An increase in sensitivity is associated with _______ in selectivity.

Currently, there are two major heuristic algorithms for performing database searches: BLAST and FASTA.

In sequence alignment by BLAST, each word from query sequence is typically _______ residues for protein sequences and _______ residues for DNA sequences.

In sequence alignment by BLAST, the second step is to search a sequence database for the occurrence of these words.

The BLAST program was developed in _______

The final step involves pairwise alignment by extending from the words in both directions while counting the alignment score using the same substitution matrix.

A recent improvement in the implementation of BLAST is the ability to provide gapped alignment.

The main application of pairwise alignment is retrieving biological sequences in databases based on similarity.

Dynamic programming method is the fastest and most practical method.

The specificity refers to the ability to include incorrect hits.

Which of the following is not one of the requirements for implementing algorithms for sequence database searching?

Sensitivity refers to the ability to find as many correct hits as possible.

The positional difference for each word between the two sequences is obtained by the position of the sequence from that of the _ sequence and is expressed as the offset.

In FASTA, For a Z-score > 15, the match can be considered extremely __ with _ of a homologous relationship.

In Smith–Waterman algorithm, in initialization Step, the _ row and column are subject to gap penalty.

BLAST uses a ___ to find matching words, whereas FASTA identifies identical matching words using the _

FASTA and BLAST are but for larger datasets.

In sequence alignment by BLAST, each word from query sequence is typically _ residues for protein sequences and _ residues for DNA sequences.