Bioinformatics Exercises
  A.Questions. Genome Sequencing
  Writer : Seyeon Weon   Updated : 10-14   Hit : 10359   Updates 

(For those who have taken the courses and want to submit for evaluation, please read the instructions linked on the table of contents page. Most of the questions below have straightforward answers from the material in the corresponding courses, although a few questions require some further studies, which are still based on the course material.)

  1. Why do we have to use the shot-gun sequencing method for genome projects?
  2. What are the major problems solved by the capillary type automatic sequencers, such as ABI 3700 and MegaBACE 1000, comparing to the slab gel type automatic sequencers?
  3. What is the definition of STS?
  4. Briefly explain the advantages of bacterial artificial chromosome (BAC) over other cloning vectors in genome sequencing.
  5. What does "golden path" stand for in the public human genome project?
  6. Genome sequencing of higher eukaryotes is much more difficult than that of prokaryotes. Besides being bigger genome size, what are the factors that make it much more difficult?
  7. What are the major characteristics of human genome which forced us to build the BAC clone tiling path first for the public human genome project? 
  8. Nowadays, above approach is no more in use. What is the method used instead? What is the main reason that makes the method our current choice?
  9. Besides the so-called whole genome shotgun (therefore, no need to do the cumbersome tiling path construction) and besides the unidirectional help from the public data, what was the major unique strategy of Celera's sequencing method? (This problem was made in 2001. I leave it here to have a chance to look back into history.)
  10. The Phred score can be used as the numerical criteria to annotate the result of a single run sequencing. For example, you can collect bands with above a certain Phred score. But, the real impact of Phred is for large scale sequencing. Briefly explain what the impact is. (This problem was made in 2001.)
  11. Why was such bizarre creature as platypus selected for genome sequencing?
  12. Why was fugu fish selected for genome sequencing?

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