ps4_sol - Solutions Systems Microbiology 1.084J/20.106J...

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Solutions Systems Microbiology 1.084J/20.106J PROBLEM SET #4 Problem 4.1 a. Describe the process of “shotgun sequencing”. Assuming an average read length of 1 kbp per individual sequence, approximately how many clones would you need to sequence to close a 10 Mbp genome? Shotgun sequencing relies on efficient and random cloning of the DNA of interest, and the generation of large numbers of clones so that the sequences can be computer assembled by looking for enough overlapping DNA fragments to cover the entire genome. b. Describe the other main alternative method for determining whole genome sequences. Are these two methods mutually exclusive? BAC sequencing utilizes larger insert clones. The BAC library is made, ordered maps of large clone contigs are made, then the BAC to be sequenced is done by shotgun sequencing followed by assembly. Problem 4.2 When the yeast nuclear genome was published the entire sequence was not completed. Additionally, the yeast mitochondrial genome proved difficult to accurately sequence. Describe in both cases the practical difficulties that were encountered during sequencing. The major difficulty in obtaining the complete sequence of the yeast nuclear genome was due to the extremely long runs of repetitive DNA and it is very difficult to accurately sequence these regions. With regard to the mitochondrial genome, there is such diversity in types that it is difficult to know “what to expect” in terms of size, codon usage, organization, etc. S. cerevisiae’s in vivo genome may be linear, further complicating the process. Problem 4.3
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This note was uploaded on 11/11/2011 for the course BIO 20.010j taught by Professor Lindagriffith during the Spring '06 term at MIT.

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ps4_sol - Solutions Systems Microbiology 1.084J/20.106J...

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