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
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)