MCQOPTIONS
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MCQOPTIONS
This section includes 78 Mcqs, each offering curated multiple-choice questions to sharpen your Bioinformatics knowledge and support exam preparation. Choose a topic below to get started.
| 51. |
Most vertebrate genes use __________ as the translation start codon and have a uniquely conserved flanking sequence call a Kozak sequence (CCGCCATGG). |
| A. | AAG |
| B. | ATG |
| C. | AUG |
| D. | AGG |
| Answer» C. AUG | |
| 52. |
In eukaryotes, gene expression is not regulated by a protein complex formed between transcription factors and RNA polymerase. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» C. May be True or False | |
| 53. |
Which of the following is a wrong statement regarding the conventional determination of open reading frames? |
| 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. | Prokaryotic DNA is first subject to conceptual translation in all six possible frames, two frames forward and four frames reverse |
| C. | A stop codon occurs in about every twenty codons by chance in a noncoding region |
| D. | Prokaryotic DNA is first subject to conceptual translation in all six possible frames, three frames forward and three frames reverse |
| Answer» C. A stop codon occurs in about every twenty codons by chance in a noncoding region | |
| 54. |
Which of the following is untrue about Homology-Based Programs? |
| A. | They are based on the fact that exon structures and exon sequences of related species are less conserved |
| B. | This approach assumes that the database sequences are correct |
| C. | It is a reasonable assumption in light of the fact that many homologous sequences to be compared with are derived from cDNA or expressed sequence tags (ESTs) of the same species |
| D. | Potential coding frames in a query sequence are translated and used to align with closest protein homologs found in databases |
| Answer» B. This approach assumes that the database sequences are correct | |
| 55. |
Once an operon structure is known ______ for the presence of a promoter and regulatory elements _____ in the operon do not possess such DNA elements. |
| A. | only the first gene is predicted, whereas other genes |
| B. | only the first hundred genes are predicted, whereas next few genes |
| C. | only first two genes are predicted, whereas next few genes |
| D. | only first ten genes are predicted, whereas next few genes |
| Answer» B. only the first hundred genes are predicted, whereas next few genes | |
| 56. |
Which of the following is untrue about FGENES? |
| A. | It stands for FindGenes |
| B. | It is a web-based program that uses LDA |
| C. | It is used to determine whether a signal is an exon |
| D. | It does not make a use of HMMs |
| Answer» E. | |
| 57. |
CpGProD is a web-based program that predicts promoters containing a high density of CpG islands _______ |
| A. | in archea genomic sequences |
| B. | in mammalian genomic sequences |
| C. | in eukaryotic and bacterial genomic sequences |
| D. | only in bacterial genomic sequences |
| Answer» C. in eukaryotic and bacterial genomic sequences | |
| 58. |
Which of the following is incorrect regarding Eponine? |
| A. | It is a web-based program that predicts transcription start sites |
| B. | It is a web-based program that particularly predicts tranpososons and retropososons |
| C. | The regulatory sites include the TATA box, the CCAAT box, and CpG islands |
| D. | It is based on a series of pre-constructed PSSMs of several regulatory sites |
| Answer» C. The regulatory sites include the TATA box, the CCAAT box, and CpG islands | |
| 59. |
Because different prediction programs have different levels of sensitivity and specificity, it makes sense to combine results of multiple programs based on consensus. This idea has prompted development of consensus-based algorithms. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 60. |
Which of the following is untrue about Prediction Using Discriminant Analysis for Gene Prediction? |
| A. | QDA draws a curved line based on a quadratic function |
| B. | LDA works by drawing a diagonal line that best separates coding signals from noncoding signals based on knowledge learned from training data sets of known gene structures |
| C. | Some gene prediction algorithms rely on discriminant analysis, either LDA or quadratic discriminant analysis (QDA), to improve accuracy |
| D. | LDA works by plotting a three-dimensional graph of coding signals versus all potential 3’ splice site positions |
| Answer» E. | |
| 61. |
The advantage of the ab initio method is that the sequence can be applied as such without having to obtain experimental information. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 62. |
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. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 63. |
Operon prediction is less important in prokaryotic promoter prediction. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» C. May be True or False | |
| 64. |
Which of the following is untrue about SGP-1? |
| A. | The program translates all potential exons in each sequence and does pair wise alignment for the translated protein sequences using a dynamic programming approach |
| B. | The near-perfect matches at the protein level define coding regions |
| C. | It is a similarity-based web program that aligns two genomic DNA sequences from distinctly related organisms |
| D. | It stands for Syntenic Gene Prediction |
| Answer» D. It stands for Syntenic Gene Prediction | |
| 65. |
Which of the following is incorrect regarding CONPRO? |
| A. | It is a web-based program that uses a consensus method |
| B. | It is used to identify promoter elements for human DNA |
| C. | cDNA does not play a role in prediction |
| D. | The program uses the information to search the human genome database for the position of the gene |
| Answer» D. The program uses the information to search the human genome database for the position of the gene | |
| 66. |
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. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 67. |
Which of the following is untrue about EST2Genome? |
| A. | It is a web-based program purely based on the sequence alignment approach to define intron–exon boundaries |
| B. | It compares an EST (or cDNA) sequence with a genomic DNA sequence containing the corresponding gene |
| C. | The alignment is rarely done using a dynamic programming–based algorithm |
| D. | Advantage of the approach is the ability to find very small exons and alternatively spliced exons that are very difficult to predict by any ab initio–type algorithms |
| Answer» D. Advantage of the approach is the ability to find very small exons and alternatively spliced exons that are very difficult to predict by any ab initio–type algorithms | |
| 68. |
Which of the following is correct regarding the method for prokaryotic operon prediction? |
| A. | 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 |
| B. | It relies only on the gene orientation and intergenic distances of a pair of genes of interest |
| C. | It relies only on the conserved linkage of the genes based on comparative genomic analysis |
| D. | The prediction cannot be done manually using the rules |
| Answer» B. It relies only on the gene orientation and intergenic distances of a pair of genes of interest | |
| 69. |
There are ____ possible stop codons, identification of which is straightforward. |
| A. | five |
| B. | two |
| C. | ten |
| D. | three |
| Answer» E. | |
| 70. |
Which of the following wrong about HMM GENE? |
| A. | It is also an HMM-based web program |
| B. | It uses a criterion called the conditional maximum likelihood to discriminate coding from non-coding features |
| C. | HMM prediction is unbiased toward the locked region |
| D. | If a sequence already has a sub-region identified as coding region, which may be based on similarity with cDNAs or proteins in a database, these regions are locked as coding regions |
| Answer» D. If a sequence already has a sub-region identified as coding region, which may be based on similarity with cDNAs or proteins in a database, these regions are locked as coding regions | |
| 71. |
Which of the following is incorrect regarding Cluster-Buster? |
| A. | It is an HMM-based web-based program |
| B. | A query sequence is scanned with a window size of 1 kb for putative regulatory motifs using motif HMMs |
| C. | It works by detecting a region of high concentration of unknown transcription factor binding sites and regulatory motifs at the initiation |
| D. | It is designed to find clusters of regulatory binding sites |
| Answer» D. It is designed to find clusters of regulatory binding sites | |
| 72. |
Which of the following is incorrect regarding First EF? |
| A. | It is a program that predicts promoters for bacterial DNA |
| B. | It is a web-based program that predicts promoters for human DNA |
| C. | It stands for First Exon Finder |
| D. | It integrates gene prediction with promoter prediction |
| Answer» B. It is a web-based program that predicts promoters for human DNA | |
| 73. |
The specific DNA sequences to which the transcription factors bind are referred to as _____ |
| A. | replication elements |
| B. | blocking factors |
| C. | transcription factors |
| D. | regulatory elements |
| Answer» E. | |
| 74. |
The homology-based method makes predictions based on significant matches of the query sequence with sequences of known genes. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 75. |
FGENESB is a web-based program that is also based on fifth-order HMMs for detecting coding regions. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 76. |
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. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 77. |
In the ab initio–based approaches—they rely on two major features associated with genes: one of them being gene content, which is statistical description of coding regions. |
| A. | True |
| B. | False |
| C. | May be True or False |
| D. | Can't say |
| Answer» B. False | |
| 78. |
Which of the following is true regarding the methods of gene prediction? |
| A. | They solely consist of a type called ab initio–based methods |
| B. | The ab initio–based approach predicts genes based on the given sequence alone |
| C. | The ab initio–based approach predicts genes based on the given sequence and relative homology data |
| D. | They solely consist of a type called homology-based approaches |
| Answer» C. The ab initio–based approach predicts genes based on the given sequence and relative homology data | |