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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?