This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Sequence Assembly and Gene Identification – 1”.
1. Sequencing of genomes depends on the assembly of a large number of DNA reads into a linear, contiguous DNA sequence.
a) True
b) False
View Answer
Explanation: The cost and efficiency of this process has been greatly improved by automatic methods of sequence assembly, first used for the sequencing of the bacterium H. influenza. This same method of assembly was also used, in part, to complete the sequencing of the Drosophila and human genomes in a timely manner.
2. Each genome sequence is scanned for protein-encoding genes using gene models trained on known gene sequences from the same organism.
a) True
b) False
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Explanation: For a new genome, each predicted gene is translated into a protein sequence; the collection of protein sequences encoded by the genome is the proteome of the organism. every protein in the proteome is then used as a query sequence in a database similarity search. Matching database sequences are realigned with the query sequence to evaluate the extent and significance of the alignment.
3. Screening the predicted protein sequences against ______ library confirms the prediction and expression of the gene.
a) expressed sequence tag (EST)
b) tags
c) palindromes
d) proteomes
View Answer
Explanation: The collective information on proteome function can then be further analyzed by self-comparison to find duplicated genes (paralogs) and by a proteome-by-proteome comparison to identify orthologs, genes that have maintained the same function through speciation, and other sequence and evolutionary relationships that are important for metabolic, regulatory, and cellular functions.
4. In case of genome sequence assembly which of the given statement is incorrect?
a) Full chromosomal sequences are assembled from the overlaps in a highly redundant set of fragments by an automatic computational method or from the fragment order on a physical map
b) Chromosome cloning is carried out in bacterial artifical chromosomes (BACs)
c) Chromosomes of a target organism are purified, fragmented, and subcloned in fragments of size hundreds of bp
d) Genome sequences are assembled from DNA sequence fragments of approximate length 500 bp obtained using DNA sequencing machines
View Answer
Explanation: Chromosomes of a target organism are purified, fragmented, and subcloned in fragments of size hundreds of kbp and not bp. The BAC fragments are then further subcloned as smaller fragments into plasmid vectors for DNA sequencing.
5. TEs (Transposable Elements) can at most comprise one-fourth of the genome sequence.
a) True
b) False
View Answer
Explanation: TEs (Transposable Elements) can comprise one-half or more of the genome sequence. Eukaryotic genomes comprise classes of repeated elements, including tandem repeats present in centromeres and telomeres, dispersed tandem repeats (minisatellites and macrosatellites), and interdispersed TEs.
6. Gene identification in prokaryotic organisms is simplified by their lacking _________
a) exons
b) introns
c) coding segments
d) useful nucleotide sequences
View Answer
Explanation: Once the sequence patterns that are characteristic of the genes in a particular prokaryotic organism (e.g, codon usage, codon neighbor preference) have been found, gene locations in the genome sequence can be predicted quite accurately. The presence of introns in eukaryotic genomes makes gene prediction more involved because, in addition to the above features, locations of intron–exon and exon–intron splice junctions must also be predicted.
7. Which of the given statement is incorrect?
a) The predicted set of proteins for the genome is referred to as the proteome
b) The amino acid sequence of proteins encoded by the predicted genes is used as a query of the protein sequence databases in a database similarity search
c) A match of a predicted protein sequence to one or more database sequences serves only to identify the gene function but it doesn’t validate the gene prediction
d) The genome sequence is annotated with the information on gene content and predicted structure, gene location, and functional predictions
View Answer
Explanation: A match of a predicted protein sequence to one or more database sequences not only serves to identify the gene function, but also validates the gene prediction. Pseudogenes, gene copies that have lost function, may also be found in this analysis.
8. Which of the following information is not directly obtained by microarray analysis?
a) Which genes are expressed at a particular stage of the cell cycle
b) Which genes are expressed at a particular stage of developmental cycle of an organism
c) Which genes are depleted at what time
d) Genes that respond to a given environmental signal to the same extent
View Answer
Explanation: For chronological information there are other numerous techniques that can be followed. This type of information provides an indication as to which genes share a related biological function or may act in the same biochemical pathway and may thereby give clues that will assist in gene identification.
9. Which of the given statement is incorrect about Functional Genomics?
a) Functional genomics involves the preparation of mutant or transgenic organisms with a mutant form of a particular gene usually designed to prevent expression of the gene
b) An abnormal properties of the mutant organism does not reveal the gene function
c) When two or more members of a gene family are found, rather than a single match to a known gene, the biological activity of these members may be analyzed by functional genomics to look for diversification of function in the family
d) A more detailed analysis of the relative amount of sequence variability in a chromosomal region within populations of closely related species can reveal the presence of genes that are under selection
View Answer
Explanation: The gene function is revealed by any abnormal properties of the mutant organism. This methodology provides a way to test a gene function that is predicted by sequence similarity to be the same as that of a gene of known function in another organism. If the other organism is very different biologically (comparing a predicted plant or animal gene to a known yeast gene), then functional genomics can also shed light on any newly acquired biological role.
10. Which of the given statement is incorrect about the gene map?
a) Gene order in two related organisms reflects the order that was present in a common ancestor genome. Chromosomal breaks followed by reassembly of fragments in a different order can produce new gene maps
b) Gene order is only revealed by the physical order of genes on the chromosome
c) Sequence variations (polymorphisms) that are close to (tightly linked) a trait may be used to trace the trait by virtue of the fact that the polymorphism and the trait are seldom separated from one generation to the next
d) These types of evolutionary changes in genomes have been modeled by computational methods
View Answer
Explanation: Gene order is revealed not only by the physical order of genes on the chromosome but also by genetic analysis. Populations of an organism show sequence variations that are readily detected by DNA sequencing and other analysis methods. The inheritance of genetic diseases in humans and animals (e.g., cancer and heart disease), and of desirable traits in plants, can be traced genetically by pedigree analysis or genetic crosses.
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