Prediction Algorithms MCQ

Test your knowledge with important Prediction Algorithms MCQ and their applications. These MCQs are beneficial for competitive exams too. Explore 30 + more Prediction Algorithms MCQs at Bissoy

Which of the following is untrue about PhyloCon?

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It stands for Phylogenetic Consensus

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It is used to identify regulatory motifs

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

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No conservation among orthologous genes and conservation among coregulated genes is a disadvantage
INCLUSive is a suite of web based tools designed to streamline the process of microarray data collection and sequence motif detection.

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True

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

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

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

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

ঘ
The basis for coexpression is thought to be due to common promoters and regulatory elements
Which of the following is untrue about FootPrinter?

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

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

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

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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 Bayes Aligner?

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

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The method generates a single best alignment

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

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It is a web-based footprinting program
rVISTA uses two orthologous sequences as input and first identifies all putative regulatory motifs based on TRANSFAC matches.

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True

খ
False
Which of the following is untrue about ConSite?

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It is a web server that finds putative promoter elements

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It includes comparing two orthologous sequences

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The program does not accept pre-computed alignment

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The program accepts pre-computed alignment
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.

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True

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

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

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

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

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It has been observed that promoter and regulatory elements from closely related organisms such as human and mouse are highly conserved
In CONPRO, for each program, the highest score prediction is taken as the promoter in the region.

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True

খ
False
Which of the following is incorrect regarding CONPRO?

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It is a web-based program that uses a consensus method

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It is used to identify promoter elements for human DNA

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cDNA does not play a role in prediction

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The program uses the information to search the human genome database for the position of the gene
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.

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True

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

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DNA bendability

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Signals such as the TATA box

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Signals such as initiator box

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Signals such as CpAA islands
McPromoter, a web-based program, uses a neural network to make promoter predictions.

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True

খ
False
Which of the following is incorrect regarding First EF?

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It is a program that predicts promoters for bacterial DNA

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It is a web-based program that predicts promoters for human DNA

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It stands for First Exon Finder

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It integrates gene prediction with promoter prediction
Which of the following is incorrect regarding Cluster-Buster?

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It is an HMM-based web-based program

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A query sequence is scanned with a window size of 1 kb for putative regulatory motifs using motif HMMs

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It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation

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It is designed to find clusters of regulatory binding sites
Which of the following is incorrect regarding Eponine?

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It is a web-based program that predicts transcription start sites

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It is a web-based program that particularly predicts tranpososons and retropososons

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The regulatory sites include the TATA box, the CCAAT box, and CpG islands

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It is based on a series of pre-constructed PSSMs of several regulatory sites
CpGProD is a web-based program that predicts promoters containing a high density of CpG islands _______

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in archea genomic sequences

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in mammalian genomic sequences

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in eukaryotic and bacterial genomic sequences

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only in bacterial genomic sequences
The eukaryotic transcription initiation is less dependent on transcription factors.

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True

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

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True

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

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The consensus patterns are only derived from bioinformatics studies

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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

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The consensus patterns are derived from experimentally determined DNA binding sites

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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 incorrect regarding FindTerm?

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

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

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

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It is available from the same site as FGENES and BPROM
In BPROM, once the operons are assigned, the program is able to predict putative promoter sequences.

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True

খ
False
Which of the following is incorrect regarding BPROM?

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

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

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It uses a linear discriminant function

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The linear discriminant function is combined with signal and content information
Which of the following is correct regarding the method for prokaryotic operon prediction?

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It relies on two kinds of information: gene orientation and intergenic distances of a pair of genes of interest and conserved linkage of the genes based on comparative genomic analysis

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It relies only on the gene orientation and intergenic distances of a pair of genes of interest

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It relies only on the conserved linkage of the genes based on comparative genomic analysis

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The prediction cannot be done manually using the rules
Once an operon structure is known ______ for the presence of a promoter and regulatory elements _____ in the operon do not possess such DNA elements.

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only the first gene is predicted, whereas other genes

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only the first hundred genes are predicted, whereas next few genes

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only first two genes are predicted, whereas next few genes

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only first ten genes are predicted, whereas next few genes
Operon prediction is less important in prokaryotic promoter prediction.

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True

খ
False
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.

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include, (0.5 to 2.0 k

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only [ include, (0.5 to 2.0 M[ only

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exclude, (0.5 to 2.0 Mb) only

ঘ
exclude, (0.5 to 2.0 kb) only
Which of the following is incorrect regarding the ab initio approaches?

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

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

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

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The consensus sequences or the matrices are relatively large, covering 700 to 1000 bases
The advantage of the ab initio method is that the sequence can be applied as such without having to obtain experimental information.

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True

খ
False