---
title: "2.1 Basics, individually"
canonical: "https://wiki.groenkennisnet.nl/space/GB/12288206/2.1%20Basics%2C%20individually"
format: markdown
---
Answer the following questions using: *[A field guide to whole-genome sequencing, assembly and annotation, Ekblom et al., 2014](https://doi.org/10.1111/eva.12178)*[.](https://doi.org/10.1111/eva.12178)

Additional information can be found on internet (for example with Google).

  


---

  


**1)    The concept ‘genome sequence’.**

a)    What are the four main problems with the concept ‘the genome sequence’?

b)    Is there a ‘true sequence’? Explain.

c)     Can a physical map of a genome ever be complete? Explain.

d)    What errors can exist in a genome sequence?

e)    How do you know if a genome sequence is correct?

  


Answers (Eckblom p1029-1030)

---

  


**2)    What is a genome sequence and what is a reference genome sequence?**

a)    Explain the term reference genome.

b)    Explain the term ‘physical map’.

c)     Explain the term ‘genetic or linkage map’.

  


Answers (Eckblom p1029)

---

  


**3)    General terms for genome sequencing and genome assembly.**

a)    What is shotgun sequencing?

b)    What is a sequence read?

c)     What is read depth?

d)    What is a contig?

e)    What is a scaffold?

f)     What is *de novo* assembly?

  


Answers (Ekblom p1030, and internet)

---

  


**4)    Assembly of a genome sequence.**

a)    What is the basis for connecting reads?

b)    What are the common steps in performing a genome assembly?

c)     How can a genetic map be used to build a physical map or a reference sequence?

d)    How can a reference sequence help to build and or use a genetic map?

e)    What is the main reason for gaps and breaks in a sequence assembly?

f)     Which type of genome (map) can you get after shotgun sequencing of an individual?

  


Answers (Ekblom p1030-1031)

---

  


**5)    Genome annotation.**

a)    Name three types of biologically relevant information that can be annotated to a genome.

b)    What is the most common type of annotation?

  


Answers (Ekblom p1036-1037, and internet)

---