Which of the following is incorrect regarding Phylogenetic Footprinting–Based Method?

It has been observed that promoter and regulatory elements from closely related organisms such as human and mouse are highly conserved

It is possible to obtain promoter sequences for a particular gene through comparative analysis

The conservation from closely related organisms is both at the sequence level and at the level of organization of the elements

The conservation from closely related organisms is most at the sequence level

It has been observed that promoter and regulatory elements from closely related organisms such as human and mouse are highly conserved

Which of the following is incorrect regarding the ab initio approaches?

The conventional approach to detecting a promoter or regulatory site is through matching a consensus sequence pattern represented by regular expressions

The conventional approach to detecting a promoter or regulatory site is through matching a position-specific scoring matrix constructed from well-characterized binding sites

The consensus sequences or the matrices are relatively short, covering 6 to 10 bases

The consensus sequences or the matrices are relatively large, covering 700 to 1000 bases

Which of the following is untrue about ConSite?

The program accepts pre-computed alignment

It is a web server that finds putative promoter elements

It includes comparing two orthologous sequences

The program does not accept pre-computed alignment

The program accepts pre-computed alignment

Which of the following is untrue about FootPrinter?

It is a web-based program for phylogenetic footprinting using multiple input sequences

The motifs from organisms spanning over the widest evolutionary distances are identified as promoter or regulatory motifs

The program performs multiple alignment of the input sequences to identify conserved motifs

The user does not necessarily provides a phylogenetic tree that defines the evolutionary relationship of the input sequences

Which of the following is untrue about PredictionUsing NeuralNetworks for Gene Prediction?

The variables in NeuralNetworks resemble the biological nervous system, with variables or nodes connected by weighted functions that are analogous to synapses

A neural network is a statistical model with a special architecture for pattern recognition and classification

It is composed of a network of mathematical variables

They resembles ab initio approaches

The variables in NeuralNetworks resemble the biological nervous system, with variables or nodes connected by weighted functions that are analogous to synapses

Which of the following is untrue about GeneMark?

If the sequence to be predicted is from a non-listed organism, the most closely related organism can be chosen as the basis for computation

It is a suite of gene prediction programs based on the fifth-order HMMs

The main program is trained on a number of complete microbial genomes

A GeneMark heuristic program can be used to improve accuracy

If the sequence to be predicted is from a non-listed organism, the most closely related organism can be chosen as the basis for computation

Which of the following is untrue about PhyloCon?

It stands for Phylogenetic Consensus

It is used to identify regulatory motifs

It is a UNIX program that combines phylogenetic footprinting with gene expression profiling analysis

No conservation among orthologous genes and conservation among coregulated genes is a disadvantage

Which of the following is a wrong statement regarding Gene Prediction Using Markov Models and Hidden Markov Models?

A zero-order Markov model assumes each base occurs independently with a given probability

Markov models and HMMs can be very helpful in providing finer statistical description of a gene

A Markov model describes the probability of the distribution of nucleotides in a DNA sequence

In a Markov model the conditional probability of a particular sequence position depends on k alternate positions

A zero-order Markov model assumes each base occurs independently with a given probability

Which of the following is untrue about Bayes Aligner?

It aligns two sequences using a Bayesian algorithm which is a unique sequence alignment method

Posterior probability values, which are considered estimates of the true alignment, are calculated for each alignment

The method generates a single best alignment

It aligns two sequences using a Bayesian algorithm which is a unique sequence alignment method

It is a web-based footprinting program

Which of the following is incorrect regarding FindTerm?

The predictions are made based on matching of known profiles of the termination signals combined with energy calculations

It is a program for searching bacterial ρ-independent termination signals located at the end of operons

It is a program for searching bacterial ρ-dependent termination signals located within the operons

The predictions are made based on matching of known profiles of the termination signals combined with energy calculations

It is available from the same site as FGENES and BPROM

Which of the following is untrue about Glimmer?

It is used to predict potential coding regions

It stands for Gene Locator and Interpolated Markov Modeler

It does not necessarily use the IMM algorithm

It is used to predict potential coding regions

Which of the following is a wrong statement regarding TESTCODE method?

This is based on the nucleotide composition of the third position of a codon

In practice, because genes can be in any of the six frames, the statistical patterns are computed for all possible frames

It is implemented in the commercial GCG package

It exploits the fact that the third codon nucleotides in a coding region fails to repeat themselves

Which of the following is untrue about Ab Initio–Based Programs for Gene Prediction?

The goal of the ab initio gene prediction programs is to discriminate exons from noncoding sequences

The goal is joining exons together in the correct order

The main difficulty is correct identification of exons

To predict exons, the algorithms rely solely on gene signals

Which of the following is untrue about translation and transcription?

The second event is splicing, which is the process of removing introns and joining exons

The first is capping is at the 5’ end of the transcript which involves methylation at the initial residue of the RNA

The splicing process involves a large RNA-protein complex called spliceosome

The second event is splicing, which is the process of removing exons and joining introns

The second event is splicing, which is the process of removing introns and joining exons

Which of the following is incorrect regarding the Prediction for Eukaryotes?

The experimentally determined DNA binding sites are compiled into profiles and stored in a database for scanning an unknown sequence to find similar conserved patterns

The consensus patterns are only derived from bioinformatics studies

The experimentally determined DNA binding sites are compiled into profiles and stored in a database for scanning an unknown sequence to find similar conserved patterns

The consensus patterns are derived from experimentally determined DNA binding sites

The ab initio method for predicting eukaryotic promoters and regulatory elements relies on searching the input sequences for matching of consensus patterns of known promoters and regulatory elements

Which of the following is untrue about Prediction Using Neural Networks for Gene Prediction?

The output is the probability of an exon structure

A neural network is constructed with multiple layers; the input, output, and hidden layers

The input is the gene sequence with intron and exon signals

The model is not fed with a sequence of known gene structure

The output is the probability of an exon structure

Which of the following is untrue about Expression Profiling–Based Method?

An advanced alignment-independent profile construction method such as EM and Gibbs motif sampling is often used in finding the subtle sequence motifs

Genes with similar expression profiles are considered coexpressed, which can be identified through a clustering approach

This approach appears to be less effective for finding transcription factor binding sites

An advanced alignment-independent profile construction method such as EM and Gibbs motif sampling is often used in finding the subtle sequence motifs

The basis for coexpression is thought to be due to common promoters and regulatory elements

Which of the following is incorrect regarding BPROM?

It uses a linear discriminant function

It is a web-based program for prediction of bacterial promoters

It is a web-based program only for prediction of eukarotic promoters

It uses a linear discriminant function

The linear discriminant function is combined with signal and content information

78 + Mcqs in Gene and Promoter Prediction in Bioinformatics Page 1 McqOptions

1.	Which of the following is incorrect regarding Phylogenetic Footprinting–Based Method?
A.	It is possible to obtain promoter sequences for a particular gene through comparative analysis
B.	The conservation from closely related organisms is both at the sequence level and at the level of organization of the elements
C.	The conservation from closely related organisms is most at the sequence level
D.	It has been observed that promoter and regulatory elements from closely related organisms such as human and mouse are highly conserved
Answer» D. It has been observed that promoter and regulatory elements from closely related organisms such as human and mouse are highly conserved

2.	Ab initio type of algorithm predicts prokaryotic and eukaryotic promoters and regulatory elements based on characteristic sequences patterns for promoters and regulatory elements.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

6.	To increase the specificity of prediction, a unique feature of eukaryotic promoter is employed, which is the presence of CpG islands.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

7.	GENSCAN is awebbased program that makes predictions based on fifth-order HMMs.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

8.	The promoter sequence may determine the expression of one gene or a number of linked genes downstream.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

10.	In bacteria, transcription is initiated by DNA polymerase.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» C. May be True or False

11.	In addition to the RNA polymerase, there are also a number of DNA-binding proteins that facilitate the process of transcription.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

12.	In bacteria, the majority of genes have a start codon ATG (orAUG in mRNA; because prediction is done at the DNA level, T is used in place of U), which codes for methionine.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

15.	The TATA box is often used as an indicator of the presence of a promoter.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

16.	In eukaryotes, genes often form an operon with a shared promoter.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

18.	In BPROM, once the operons are assigned, the program is able to predict putative promoter sequences.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

31.	To improve the specificity of prediction, some algorithms selectively ______ coding regions and focus on the upstream regions________ which are most likely to contain promoters. In that sense, promoter prediction and gene prediction are coupled.
A.	include, (0.5 to 2.0 kb) only
B.	include, (0.5 to 2.0 Mb) only
C.	exclude, (0.5 to 2.0 Mb) only
D.	exclude, (0.5 to 2.0 kb) only
Answer» E.

20.	The putative ORF can be translated into a protein sequence, which is then used to search against a protein database.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

21.	Because a protein-encoding gene is composed of nucleotides in triplets as codons, more effective Markov models are built in sets of three nucleotides, describing nonrandom distributions of trimers or hexamers, and so on.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

22.	The use of Markov models in gene finding exploits the fact that oligonucleotide distributions in the coding regions are different from those for the noncoding regions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

23.	A caveat of phylogenetic footprinting is to extract noncoding sequences Upstream of corresponding genes and focus the comparison to this region only, which helps to prevent false positives.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

24.	The input for the neural network includes parameters for sequence physical properties, such as ______
A.	DNA bendability
B.	Signals such as the TATA box
C.	Signals such as initiator box
D.	Signals such as CpAA islands
Answer» E.

26.	INCLUSive is a suite of web based tools designed to streamline the process of microarray data collection and sequence motif detection.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

27.	McPromoter, a web-based program, uses a neural network to make promoter predictions.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

28.	Shine-Delgarno sequence, which is a stretch of purine-rich sequence complementary to 16S rRNA in the ribosome.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

29.	The main issue in prediction of eukaryotic genes is the identification of exons, introns, and splicing sites.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

30.	The upstream sequence where the σ protein binds constitutes the promoter sequence.
A.	True
B.	False
C.	May be True or False
D.	Can't say
Answer» B. False

Explore topic-wise MCQs in Bioinformatics.

Which of the following is incorrect regarding Phylogenetic Footprinting–Based Method?

Ab initio type of algorithm predicts prokaryotic and eukaryotic promoters and regulatory elements based on characteristic sequences patterns for promoters and regulatory elements.

Which of the following is incorrect regarding the ab initio approaches?

Which of the following is untrue about ConSite?

Which of the following is untrue about FootPrinter?

To increase the specificity of prediction, a unique feature of eukaryotic promoter is employed, which is the presence of CpG islands.

GENSCAN is awebbased program that makes predictions based on fifth-order HMMs.

The promoter sequence may determine the expression of one gene or a number of linked genes downstream.

Which of the following is untrue about PredictionUsing NeuralNetworks for Gene Prediction?

In bacteria, transcription is initiated by DNA polymerase.

In addition to the RNA polymerase, there are also a number of DNA-binding proteins that facilitate the process of transcription.

In bacteria, the majority of genes have a start codon ATG (orAUG in mRNA; because prediction is done at the DNA level, T is used in place of U), which codes for methionine.

Which of the following is untrue about GeneMark?

Which of the following is untrue about PhyloCon?

The TATA box is often used as an indicator of the presence of a promoter.

In eukaryotes, genes often form an operon with a shared promoter.

Which of the following is a wrong statement regarding Gene Prediction Using Markov Models and Hidden Markov Models?

In BPROM, once the operons are assigned, the program is able to predict putative promoter sequences.

Which of the following is untrue about Bayes Aligner?

The putative ORF can be translated into a protein sequence, which is then used to search against a protein database.

Because a protein-encoding gene is composed of nucleotides in triplets as codons, more effective Markov models are built in sets of three nucleotides, describing nonrandom distributions of trimers or hexamers, and so on.

The use of Markov models in gene finding exploits the fact that oligonucleotide distributions in the coding regions are different from those for the noncoding regions.

A caveat of phylogenetic footprinting is to extract noncoding sequences Upstream of corresponding genes and focus the comparison to this region only, which helps to prevent false positives.

The input for the neural network includes parameters for sequence physical properties, such as ______

Which of the following is incorrect regarding FindTerm?

INCLUSive is a suite of web based tools designed to streamline the process of microarray data collection and sequence motif detection.

McPromoter, a web-based program, uses a neural network to make promoter predictions.

Shine-Delgarno sequence, which is a stretch of purine-rich sequence complementary to 16S rRNA in the ribosome.

The main issue in prediction of eukaryotic genes is the identification of exons, introns, and splicing sites.

The upstream sequence where the σ protein binds constitutes the promoter sequence.

To improve the specificity of prediction, some algorithms selectively ______ coding regions and focus on the upstream regions________ which are most likely to contain promoters. In that sense, promoter prediction and gene prediction are coupled.

The eukaryotic transcription initiation is less dependent on transcription factors.

TwinScan is also a similarity-based gene-finding Server and it is similar to GenomeScan in that it uses GenScan to predict all possible exons from the genomic sequence.

In Ab Initio–Based Programs for Gene Prediction– Gene content refers to coding statistics, which includes nonrandom nucleotide distribution, amino acid distribution, synonymous codon usage, and hexamer frequencies.

Which of the following is untrue about Glimmer?

Which of the following is a wrong statement regarding TESTCODE method?

GenomeScan is a web-based server that combines GENSCAN prediction results with BLASTX similarity searches.

The drawback of Homology-based approach is its reliance on the presence of homologs in databases.

Which of the following is untrue about Ab Initio–Based Programs for Gene Prediction?

The presence of these codons at The beginning of the frame _____ give a clear indication of the translation initiation site.

Which of the following is untrue about translation and transcription?

GRAIL is a web-based program that is based on a neural network algorithm Which is trained on several statistical features such as splice junctions, start and stop codons, poly-A sites, promoters, and CpG islands.

rVISTA uses two orthologous sequences as input and first identifies all putative regulatory motifs based on TRANSFAC matches.

Eukaryotic RNA polymerase II does not directly bind to the promoter, but relies on a dozen or more transcription factors to recognize and bind to the promoter in a specific order before its own binding around the promoter.

Which of the following is incorrect regarding the Prediction for Eukaryotes?

Which of the following is untrue about Prediction Using Neural Networks for Gene Prediction?

In CONPRO, for each program, the highest score prediction is taken as the promoter in the region.

Which of the following is untrue about Expression Profiling–Based Method?

Which of the following is incorrect regarding BPROM?

TSSW is a web program that distinguishes promoter sequences from non-promoter sequences based on a combination of unique content information such as hexamer/trimer frequencies and signal information such the TATA box in the promoter region.

To improve the specificity of prediction, some algorithms selectively coding regions and focus on the upstream regions__ which are most likely to contain promoters. In that sense, promoter prediction and gene prediction are coupled.

35.	Which of the following is untrue about Glimmer?
A.	It stands for Gene Locator and Interpolated Markov Modeler
B.	It is a UNIX program from TIGR
C.	It does not necessarily use the IMM algorithm
D.	It is used to predict potential coding regions
Answer» D. It is used to predict potential coding regions

40.	The presence of these codons at The beginning of the frame _____ give a clear indication of the translation initiation site.
A.	always
B.	does not necessarily
C.	does not
D.	never
Answer» C. does not