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The correct answer is (c) both, a certain range, clone

To EXPLAIN: A COMMONLY used constraint to avoid errors CAUSED by sequence repeats is the so called forward–reverse constraint. When the constraint is applied, EVEN when one of the fragments has a perfect match with a repetitive element outside the range, it is not able to be moved to that location to cause miss-assembly.

Correct answer is (B) It doesn’t take input from Phred

For explanation: It takes Phred BASE-call files with quality scores as input and aligns individual fragments in a pairwise fashion USING the Smith–Waterman algorithm. The base quality information is taken into account during the pairwise alignment. After all the pair wise sequence similarity is identified, the program performs assembly by progressively merging sequence pairs with decreasing similarity scores while removing overlapped regions. Consensus contigs are DERIVED after joining all possible overlapped READS.

Right option is (a) True

To explain: 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.

Right OPTION is (a) physical, the LOCATIONS and orders

Easiest 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.

Right answer is (c) The automated APPROACH doesn’t rely on heuristic sequence similarity searching

Best EXPLANATION: If a NEWLY sequenced gene or its gene product has significant matches with a database sequence BEYOND a certain threshold, a transfer of functional assignment is taking place. In addition to sequence matching at the full length, detection of conserved motifs OFTEN offers additional functional clues.

Correct choice is (d) very LOW, inaccurate

The explanation: The banding patterns, however, are not always constant and are SUBJECT to change depending on the extent of chromosomal contraction. Thus, cytologic maps can be considered to be of very low resolution and hence SOMEWHAT inaccurate physical maps. The distance between two BANDS is expressed in relative units (Dustin units).

The correct answer is (a) True

The best I can explain: It USES a number of radio labeled probes to hybridize to a library of DNA CLONE fragments. By identifying overlapping CLONES probed by common probes, a relative order of the CLONED fragments can be established.

Right ANSWER is (a) It is also known as vertical gene transfer

For explanation: It is defined as the exchange of genetic materials between species in a way that is incongruent with commonly accepted vertical evolutionary pathway. Examples are transformation (direct uptake of foreign DNA from environment), conjugation (gene uptake through mating behavior), and transduction (gene uptake mediated by infecting VIRUSES). The TRANSMISSION of genes between organisms can occur relatively RECENTLY or as a more ancient event.

The CORRECT CHOICE is (d) minimal

The explanation: Finding minimal genomes helps provide an understanding of genes constituting KEY metabolic PATHWAYS, which are critical for a cell’s survival. This analysis involves identification of orthologous genes shared between a number of divergent genomes.

Right option is (d) There is no identifying overlap between SEQUENCE fragments

The explanation: ONE of the steps includes identifying overlaps between sequence fragments, assigning the order of the fragments and DERIVING a consensus of an overall sequence. Assembling all shotgun fragments into a full genome is a computationally very challenging step. There are a variety of programs available for PROCESSING the raw sequence data.

Correct option is (d) similar to the shotgun approach, but on a smaller scale

The 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).

Correct OPTION is (a) one

To explain I WOULD say: One centiMorgan is one percentage of the total recombination events when separation of the two genetic markers is observed in a genetic CROSSING experiment. One centiMorgan is approximately 1 Mb in humans and 0.5 Mb in DROSOPHILA.

Right answer is (a) True

For explanation: Single or oligonucleotide STATISTICS, such as G–C composition, codon BIAS, and oligonucleotide frequencies are used. Unusual nucleotide statistics in certain genomic REGIONS versus the rest of the genome may help to identify “foreign” genes in a genome. A commonly used parameter is GC skew ((G − C)/(G + C)), which is compositional bias for G in a DNA sequence and is a commonly used indicator for newly acquired GENETIC elements.

Right CHOICE is (b) This doesn’t make use of DNA polymerases

To ELABORATE: 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.

The correct answer is (C) It provides INSIGHTS into the MECHANISM of genome evolution and gene transfer among genomes

Easiest explanation: It helps to understand the PATTERN of acquisition of foreign genes through lateral gene transfer. It also helps to reveal the core set of genes common among different genomes, which should correspond to the genes that are crucial for survival. This knowledge can be potentially useful in future METABOLIC pathway engineering.

Correct choice is (d) slower, more costly

For 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.

The correct answer is (a) They cannot be directly OBSERVED under MICROSCOPE

Best explanation: Cytologic maps refer to banding PATTERNS SEEN on stained chromosomes, which can be directly observed under a microscope. The observable LIGHT and dark bands are the visually distinct markers on a chromosome.

Correct answer is (d) It doesn’t involve heuristic approach

For explanation: Its unique features include using a heuristic approach similar to FASTA to align overlapping FRAGMENTS, evaluating alignments using statistical SCORES, correcting sequencing errors based on multiple sequence ALIGNMENT, and using forward-reverse constraints. It accepts base calls with associated quality scores assigned by Phred as INPUT and produces scaffolds or a FULLY assembled genome.

The correct option is (C) regardless of

The best I can EXPLAIN: The distance between GENETIC MARKERS is measured directly as kilobases (Kb) or megabases (Mb). Because the distance is EXPRESSED in physical units, it is more accurate and reliable than centiMorgans used in genetic maps.

Right option is (a) It is a web SERVER for protein DNA annotation

For explanation: It PERFORMS domain analysis USING the PROSITE and Blocks databases as well as analysis of secondary structures and super-secondary structures that include prediction of coiled coils and transmembrane helices. Multiple search and analysis results are compiled to produce a summary of protein function with an assigned confidence level (clear, tentative, marginal, and negligible).

The correct choice is (b) Generally, gene ORDER is much more conserved compared with gene sequences

Explanation: Gene order conservation is in FACT rarely OBSERVED among divergent species. Therefore, comparison of syntenic relationships is normally carried out between relatively close LINEAGES. However, if syntenic relationships for certain genes are indeed observed among divergent prokaryotes, they often provide important CLUES to functional relationships of the genes of interest.

Correct option is (a) True

To explain: 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.

The correct OPTION is (d) The pairwise alignment programs are not involved

The explanation: The predictions are VERIFIED by BLAST searches against a sequence database. The PREDICTED genes are further COMPARED with experimentally DETERMINED cDNA and EST sequences using the pairwise alignment programs such as GeneWise, Spidey, SIM4, and EST2 Genome.

Right choice is (a) True

To EXPLAIN I would say: It treats the sequence INPUT as clean reads without consideration of the sequence quality. A main feature of the PROGRAM is the application of the forward–reverse constraints to avoid miss-ASSEMBLY caused by sequence REPEATS. The sequence alignment in the assembly stage is performed using the Smith–Waterman algorithm.

Right answer is (a) True

To elaborate: Sequence errors can often be corrected by drawing a consensus from an alignment of multiple overlapped sequences. Bacterial vector sequences can be removed using filtering programs prior to assembly. To overcome the problem of sequence REPEATS, programs such as RepeatMasker can be used to DETECT and mask repeats. ADDITIONAL constraints on the sequence reads can be APPLIED to avoid miss-assembly caused by repeat sequences.

The correct answer is (a) True

Easy EXPLANATION: Once the gene is cloned, the determination of DNA SEQUENCE is POSSIBLE. Further, the STUDY of target PROTEIN is carried out.

Correct option is (a) True

For explanation I WOULD say: The rationale behind genetic MAPPING is that the closer the two genetic MARKERS are, the more likely it is that they are inherited together and are not separated in a genetic crossing event. The distance between the two genetic markers is measured in centiMorgans (cM), which is the FREQUENCY of recombination of genetic markers.

The correct choice is (a) True

For explanation I would say: Detecting remote homologs typically INVOLVES combined searches of protein motifs and domains and PREDICTION for secondary and tertiary structures. The prediction can also be performed USING structure-based approaches such as THREADING and fold recognition.

The correct choice is (b) There is no standardization of ASSOCIATED PATHWAYS

To EXPLAIN: A GO description of a protein provides three sets of information: biological PROCESS, cellular component, and molecular function, each of which uses a unique set of non-overlapping vocabularies. The standardization of the names, activities, and associated pathways provides consistency in DESCRIBING overall protein functions.

The correct choice is (a) True

The explanation: The PRESERVATION of the GENE order is a result of the selective pressure to allow the genes to be co-regulated and function as an operon. Furthermore, the SYNTENY of genes from divergent groups OFTEN associates with physical interactions of the encoded gene products.

Correct option is (d) both RECENT and ancient lateral gene transfer events

The best I can explain: Abnormal groupings in phylogenetic TREES are often interpreted as the possibility of lateral gene transfer events. There are some basic TOOLS for identifying genomic REGIONS that MAY be a result of lateral gene transfer events using the within-genome approach, namely, ACT, Swaap.

Correct choice is (c) core, four

For explanation: The user supplies NCBI accession numbers for the genomes of INTEREST. The PROGRAM performs an iterative BLAST comparison to find orthologous genes by using one GENOME as a reference and another as a QUERY. This pairwise comparison is performed for all four genomes. As a result, the COMMON genes are compiled as a core set of genes from the genomes.

Correct ANSWER is (c) identifiable, chromosome

The best explanation: For many EUKARYOTES, GENETIC markers represent morphologic phenotypes. In addition to genetic linkage maps, there are also other types of GENOME maps such as physical maps and cytologic maps, which describe GENOMES at different levels of resolution.

The correct CHOICE is (c) In this approach, a sequence fragment is broken down to tuples of five nucleotides

The explanation: The tuples are converted to binary vectors in the nodes. By using a Viterbi algorithm, the shortest path among the vectors can be found, which is the best WAY to connect the tuples into a full sequence. Because this approach does not directly rely on detecting OVERLAPS, it may be advantageous in assembling SEQUENCES with repeat MOTIFS.

The correct choice is (b) It doesn’t give a probability score in output

The explanation is: It also gives a probability score for each base call that may be ATTRIBUTABLE to error. The commonly accepted score threshold is TWENTY, which corresponds to a 1% chance of error. The HIGHER the score, the better the quality of the sequence reads. If the score VALUE falls below the threshold, human INTERVENTION is required.

The correct option is (b) It is a web-based program designed for pairwise ALIGNMENT of small FRAGMENTS of genomes only

Explanation: It is a web-based program designed for pairwise alignment of large genomes. The unique feature of this program is that it is able to take into ACCOUNT degeneracy of the genetic CODES and is therefore able to handle more distantly related genomes.

Right option is (b) This is a major strategy that eukaryotic organisms USE to achieve a myriad of genotypic diversities only

To elaborate: A major mechanism responsible for the protein diversity is alternative SPLICING, which refers to the splicing event that joins different exons from a single gene to FORM different transcripts. A RELATED mechanism, known as exon shuffling, which joins exons from different genes to generate more transcripts, is also common in eukaryotes. It is known that, in humans, about two THIRDS of the genes exhibit alternative splicing and exon shuffling during expression, generating 90% of the total proteins.

The CORRECT option is (a) HIGHEST, PHYSICAL

Easy EXPLANATION: Cytological maps have quite low resolution, when compared to physical maps. They can be viewed under microscopes as well.

The correct option is (a) True

For EXPLANATION: Before the assembled sequence is DEPOSITED into a DATABASE, it has to be analyzed for useful biological features. The GENOME annotation process provides comments for the features.

Right choice is (b) It doesn’t HELP to understand sequence conservation between genomes

The BEST explanation: Regular alignment programs tend to be error prone and inefficient when dealing with long stretches of DNA containing HUNDREDS or THOUSANDS of genes. Another challenge of genome alignment is effective visualization of alignment results. Because it is obviously difficult to sift through and make sense of the extremely large alignments, a graphical representation is a MUST for interpretation of the result.

Right answer is (B) False

Explanation: It is a web-based PROGRAM that HELPS DETECT contaminating bacterial vector sequences. It scans an input nucleotide sequence and compares it with a database of known vector sequences by USING the BLAST program.

Correct answer is (a) True

Best explanation: This process is CALLED base calling. Automated base calling may generate errors and human intervention is OFTEN required to correct the SEQUENCE calls.

Correct answer is (c) The average length of the reads is about 50 bases

The BEST I can explain: The average length of the reads is about 500 bases. To assemble a whole GENOME sequence, these short fragments are joined to form LARGER fragments after removing overlaps. These longer, merged sequences are termed contigs, which are usually 5,000 to 10,000 bases long. A number of OVERLAPPING contigs can be further merged to form scaffolds (30,000–50,000 bases, also called supercontigs), which are unidirectionally oriented along a physical map of a chromosome.

Right option is (a) True

Easy 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.