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BME130 – Midterm 1
11 October 2011
NAME:
1. Construct a de Bruijn graph of k-mer length 6 of the following sequence reads:
R1.
R2.
R3.
2. Construct a de Bruijn graph of k-mer length 5 of the same reads.
3. What are the benefits of using longer k-mers in de Bruijn graphs
for sequence assembly?
4. What are the drawbacks of using longer k-mers in de Bruijn graphs
for sequence assembly?
5. Make a recombination map from the following genetic cross:
6. How many homopolymers are in this sequence:
5’-ATGGAATAGGCG-3’
7. If the base flow-order in 454 sequencing is T, A, C, G, T, A, C,
G, …, how many positive (non-zero) signals many rounds (cycle of
each of the four bases) of base flows would one need to sequence
the DNA shown above?
8. A fosmid DNA sequence was digested with two, type II DNA
endonucleases, EcoRI and SalI. The restriction products were run
on an agarose gel and had these lengths:
EcoRI: 10 kb, 8kb, and 21kb
SalI: 15kb, 24kb
What is the total length of the fosmid?
9. A double digestion, using both enzymes was then done. The
restriction products had these lengths:
[]
Draw a restriction map of this fosmid.
10.
Name two ways that Solexa/Illumina sequencing differs from
Roche/454 sequencing.
11.
Which is an appropriate cloning vector for a piece of DNA
that is 100 kilobases long?
12.
What is the answer to the secret question?
13.
Describe the difference between a sequence gap and a
physical gap in genome assembly. Which does not require a new
clone library to be constructed in order to close?