This set of Bioinformatics Multiple Choice Questions & Answers (MCQs) focuses on “Genome Sequencing”.
1. The _____ resolution genome map is the genomic DNA sequence that can be considered as a type of ______ map describing a genome at the single base-pair level.
a) highest, physical
b) lowest, physical
c) highest, cytological
d) lowest, cytological
Explanation: Cytological maps have quite low resolution, when compared to physical maps. They can be viewed under microscopes as well.
2. Which of the following is untrue about DNA sequencing?
a) It is now routinely carried out using the Sanger method
b) This doesn’t make use of DNA polymerases
c) This involves synthesis of DNA chains of varying length
d) The DNA synthesis is stopped by adding dideoxynucleotides
Explanation: DNA polymerases are used to synthesize DNA chains. The dideoxynucleotides are labeled with fluorescent dyes, which terminate the DNA synthesis at positions containing all four bases, resulting in nested fragments that vary in length by a single base. When the labeled DNA is subjected to electrophoresis, the banding patterns in the gel reveal the DNA sequence.
3. In DNA sequencing, the fluorescent traces of the DNA sequences are read by a computer program that assigns bases for each peak in a chromatogram.
Explanation: This process is called base calling. Automated base calling may generate errors and human intervention is often required to correct the sequence calls.
4. The shotgun approach _______ sequences clones from _____ of cloned DNA.
a) randomly, one end
b) randomly, both ends
c) specifically, both ends
d) specifically, one end
Explanation: There are two major strategies for whole genome sequencing: the shotgun approach and the hierarchical approach. The shotgun approach generates a large number of sequenced DNA fragments. The number of random fragments has to be very large, so large that the DNA fragments overlap sufficiently to cover the entire genome.
5. The shotgun approach does not require knowledge of physical mapping of the clone fragments, but rather a robust computer assembly program to join the pieces of random fragments into a single, whole-genome sequence.
Explanation: Generally, the genome has to be redundantly sequenced in such a way that the overall length of the fragments covers the entire genome multiple times. This is designed to minimize sequencing errors and ensure correct assembly of a contiguous sequence. Overlapping sequences with an overall length of six to ten times the genome size are normally obtained for this purpose.
6. Despite the multiple coverage, sometimes certain genomic regions remain unsequenced, mainly owing to cloning difficulties.
Explanation: In such mentioned cases, the remainder gap sequences can be obtained through extending sequences from regions of known genomic sequences using a more traditional PCR technique. That which requires the use of custom primers and performs genome walking in a stepwise fashion. This step of genome sequencing is also known as finishing, which is followed by computational assembly of all the sequence data into a final complete genome.
7. The hierarchical genome sequencing approach is ______
a) entirely dissimilar to the shotgun approach
b) dissimilar to the shotgun approach
c) similar to the shotgun approach, but on a larger scale
d) similar to the shotgun approach, but on a smaller scale
Explanation: In this, the chromosomes are initially mapped using the physical mapping strategy. Longer fragments of genomic DNA (100 to 300 kB) are obtained and cloned into a high-capacity bacterial vector called bacterial artificial chromosome (BAC).
8. In hierarchical genome sequencing approach, based on the results of _______ mapping, _______of the BAC clones on a chromosome can be determined.
a) physical, the locations and orders
b) physical, only the locations
c) cytological, only the locations
d) physical, only the orders
Explanation: By successively sequencing adjacent BACclone fragments, the entire genome can be covered. The complete sequence of each individual BAC clone can be obtained using the shotgun approach. Overlapping BAC clones are subsequently assembled into an entire genome sequence.
9. The hierarchical approach is ____ and _____ than the shotgun approach because it involves an initial clone-based physical mapping step.
a) slower, less costly
b) faster, more costly
c) faster, less costly
d) slower, more costly
Explanation: During the era of human genome sequencing, there was a heated debate on the merits of each of the two strategies. Despite the mentioned fact, once the map is generated, assembly of the whole genome becomes relatively easy and less error prone.
10. The whole genome shotgun approach can produce a draft sequence very rapidly because it is based on the direct sequencing approach.
Explanation: However, it is computationally very demanding to assemble the short random fragments. Although the approach has been successfully employed in sequencing small microbial genomes, for a complex eukaryotic genome that contains high levels of repetitive sequences, such as the human genome, the full shotgun approach becomes less accurate and tends to leave more “holes” in the final assembled sequence than the hierarchical approach. Current genome sequencing of large organisms often uses a combination of both approaches.
Sanfoundry Global Education & Learning Series – Bioinformatics.
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