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This quiz contains multiple-choice problems on prediction algorithms and promoter and regulatory elements in prokaryotes and eukaryotes.
In bacteria, transcription is initiated by DNA polymerase. True or false?
True
False
The specific DNA sequences to which the transcription factors bind are referred to as
Replication elements
Blocking factors
Transcription factors
Regulatory elements
Which of the following is incorrect?
RNA polymerases I is responsible for the transcription of ribosomal RNA
RNA polymerases III is responsible for the transcription of tRNA
RNA polymerase II is exclusively responsible for transcribing protein-encoding genes
Synthesis of mRNAs is carried out by RNA polymerase I
The upstream sequence with which the σ protein binds constitutes the promoter sequence. True or false?
True
False
The promoter sequence may determine the expression of one gene or several linked genes downstream. True or false?
True
False
The eukaryotic transcription initiation is less dependent on transcription factors. True or false?
True
False
CpGProD is a web-based program that predicts the promoters containing a high density of CpG islands
In archaea genomic sequences
In mammalian genomic sequences
In eukaryotic and bacterial genomic sequences
Only in bacterial genomic sequences
Which of the following is incorrect regarding Eponine?
It is a web-based program that predicts transcription start sites
It is a web-based program that particularly predicts tranpososons and retropososons
The regulatory sites include the TATA box, the CCAAT box, and CpG islands
It is based on a series of pre-constructed PSSMs of several regulatory sites
Which of the following is incorrect regarding Cluster-Buster?
It is an HMM-based web-based program
A query sequence is scanned with a window size of 1 kb for putative regulatory motifs using motif HMMs
It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation
It is designed to find clusters of regulatory binding sites
Which of the following is incorrect regarding First EF?
It is a program that predicts promoters for bacterial DNA
It is a web-based program that predicts promoters for human DNA
It stands for First Exon Finder
It integrates gene prediction with promoter prediction
McPromoter, a web-based program, uses a neural network to make promoter predictions. True or false?
True
False
The inputs for the neural network include parameters for sequence physical properties, such as
DNA bendability
Signals such as the TATA box
Signals such as initiator box
Signals such as CpAA islands
TSSW is a web program that distinguishes promoter sequences from non-promoter sequences based on unique content information such as hexamer/trimer frequencies and signal information such as the TATA box in the promoter region. True or false?
True
False
Which of the following is incorrect regarding COMPRO?
It is a web-based program that uses a consensus method
It is used to identify promoter elements for human DNA
cDNA does not play a role in prediction
The program uses the information to search the human genome database for the position of the gene
In COMPRO, the highest score prediction is taken as the promoter in the region for each program. True or false?
True
False
