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Gene and Promoter Prediction Online Exam Quiz

Important questions about Gene and Promoter Prediction. Gene and Promoter Prediction MCQ questions with answers. Gene and Promoter Prediction exam questions and answers for students and interviews.

Which of the following is true regarding the methods of gene prediction?

Options

A : a. They solely consist of a type called ab initio–based methods

B : b. The ab initio–based approach predicts genes based on the given sequence alone

C : c. The ab initio–based approach predicts genes based on the given sequence and relative homology data

D : d. They solely consist of a type called homology-based approaches

In the ab initio–based approaches—they rely on two major features associated with genes: one of them being the existence of gene signals, which include start and stop codons, intron splice signals, transcription factor binding sites, etc.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

The homology-based method makes predictions based on significant matches of the query sequence with sequences of known genes.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

FGENESB is a web-based program that is also based on fifth-order HMMs for detecting coding regions.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about GeneMark?

Options

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

B : b. The main program is trained on a number of complete microbial genomes

C : c. A GeneMark heuristic program can be used to improve accuracy

D : d. 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 Glimmer?

Options

A : a. It stands for Gene Locator and Interpolated Markov Modeler

B : b. It is a UNIX program from TIGR

C : c. It does not necessarily use the IMM algorithm

D : d. It is used to predict potential coding regions

RBS finder is a UNIX program that uses the prediction output from Glimmer and searches for the Shine–Delgarno sequences in the vicinity of predicted start sites.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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

Options

A : a. always

B : b. does not necessarily

C : c. does not

D : d. never

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

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

There are ____ possible stop codons, identification of which is straightforward.

Options

A : a. five

B : b. two

C : c. ten

D : d. three

Which of the following is a wrong statement regarding the conventional determination of open reading frames?

Options

A : a. Without the use of specialized programs, prokaryotic gene identification can rely on manual determination of ORFs and major signals related to prokaryotic genes

B : b. Prokaryotic DNA is first subject to conceptual translation in all six possible frames, two frames forward and four frames reverse

C : c. A stop codon occurs in about every twenty codons by chance in a noncoding region

D : d. Prokaryotic DNA is first subject to conceptual translation in all six possible frames, three frames forward and three frames reverse

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

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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

Options

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

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

C : c. It is implemented in the commercial GCG package

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

The conventional determination of open reading methods identify only typical genes and tend to miss atypical genes in which the rule of codon bias is not strictly followed.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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

Options

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

B : b. A Markov model describes the probability of the distribution of nucleotides in a DNA sequence

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

D : d. A zero-order Markov model assumes each base occurs independently with a given probability

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.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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.

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

Which of the following is untrue about translation and transcription?

Options

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

B : b. The splicing process involves a large RNA-protein complex called spliceosome

C : c. The second event is splicing, which is the process of removing exons and joining introns

D : d. The second event is splicing, which is the process of removing introns and joining exons

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

Options

A : a. True

B : b. False

C : c. May be True or False

D : d. Can't say

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