Q: If you have 1 million reads, each 350 bp long, and a genome of 35,000,000 bp, what is the coverage?

$C = \frac{1,000,000 \times 350}{35,000,000} = 10$

Question 1

Which of the following best describes the main difference between Sanger sequencing and Illumina sequencing?

Accepted Answer

Sanger sequencing generates one read per reaction using chain-terminating nucleotides, while Illumina sequencing generates millions of short reads simultaneously using bridge amplification.

Question 2

In Sanger sequencing, what is the role of dideoxynucleotides (ddNTPs)?

Accepted Answer

They terminate DNA strand synthesis by preventing addition of further nucleotides.

Question 3

Which equation correctly calculates sequencing coverage ($C$) given $N$ reads, average read length $L$, and genome length $G$?

Accepted Answer

$C = \frac{N 	imes L}{G}$

Question 4

A FASTQ file contains which two types of information for each sequencing read?

Accepted Answer

Read sequence and quality score

Question 5

What is the main challenge posed by repetitive DNA sequences when assembling genomes using Illumina sequencing?

Accepted Answer

Repeats can cause misassembly because short reads cannot span the entire repeat region.

Question 6

Which statement about Oxford Nanopore sequencing is correct?

Accepted Answer

It sequences DNA by measuring changes in electrical current as DNA passes through a synthetic membrane.

Question 7

If you have 1 million reads, each 350 bp long, and a genome of 35,000,000 bp, what is the coverage?

Accepted Answer

$C = \frac{1,000,000 	imes 350}{35,000,000} = 10$

Question 8

Which of the following is a key feature of intrinsic (ab initio) gene annotation methods?

Accepted Answer

They identify gene boundaries and predicted protein lengths using only the raw DNA sequence.

Question 9

What is the main output of extrinsic gene annotation methods?

Accepted Answer

Information about gene function and experimental evidence for gene expression

Question 10

Which annotation software tool is best suited for prokaryotic genome annotation and integrates both intrinsic and extrinsic methods?

Accepted Answer

PROKKA

Question 11

In Illumina sequencing, what is the purpose of bridge amplification?

Accepted Answer

To amplify DNA fragments on a flow cell, creating clusters for sequencing

Question 12

Which of the following best explains why combining Illumina and Nanopore reads improves genome assembly?

Accepted Answer

Short Illumina reads provide high accuracy, while long Nanopore reads span repetitive regions and resolve complex structures.

Question 13

Which of the following is NOT a direct method for measuring gene expression?

Accepted Answer

Microarrays

Question 14

What does a Q30 quality score in Sanger sequencing indicate?

Accepted Answer

A 1% chance of error (99% accuracy)

Question 15

Which of the following is a limitation of Illumina sequencing when assembling whole genomes?

Accepted Answer

Short read lengths make it difficult to resolve large repetitive regions

Question 16

Which method would you use to experimentally validate the presence of introns in a eukaryotic gene?

Accepted Answer

RNA-seq

Question 17

What is the main advantage of using proteomics as an extrinsic method in genome annotation?

Accepted Answer

It identifies proteins produced in a sample, confirming gene expression and function.

Question 18

Which of the following is true about the central dogma of molecular biology?

Accepted Answer

DNA is transcribed to RNA, which is translated to protein.

Question 19

Which feature distinguishes eukaryotic gene structure from prokaryotic gene structure?

Accepted Answer

Presence of introns and exons, with introns removed by splicing in eukaryotes

DNA Sequencing and Gene Annotation: Methods and Applications in Biochemistry

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