Bioinformatics Exercises
  B.Problems. Comparative Genomics
  Writer : Seyeon Weon   Updated : 10-14   Hit : 2450   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.)

  1. Answer the following questions about genome scale global alignment: (Within 10 lines for each)
    1. What are the major reasons that make it a computational hard problem?
    2. However, for example, the genome scale global alignment between human and mouse can be done using some heuristic. What would be the biological reason that makes it work?
    3. Why is “global” alignment of “genomic” sequence important?

  2. In practice, there is an intrinsic weakness that is common to all phylogenomic methods, such as phylogenetic profile method, Rosetta stone method, and gene cluster method. What is it? Among these three methods, which one would you think provides the strongest evidence for function prediction in general? Explain why.

  3. Phylogenetic profile, gene fusion, and gene cluster are the methods used to infer the functional relation between genes. However, this type of methods can be hindered by the existence of paralogs. Think about some ways to overcome or minimize it.

  4. The information about the ENCODE project can be found at http://www.genome.gov/10005107. Also read the article in Nature titled “A vision for the future of genomics research” and the URL for the article is http://www.nature.com/cgi-taf/DynaPage.taf?file=/nature/journal/v422/n6934/full/nature01626_fs.html. Write your own opinion about the following questions: (Within 10 lines for each)
    1. Why is finding noncoding elements in genomic sequences difficult?
    2. How can the so-called comparative genomics help for that and what could be the limitation of it?
    3. What would be the major reasons that make finding microRNA, which may the most prominent success story of the comparative genomics so far, possible?
    4. Do you think if there is any other major regulatory paradigm, which has not been found yet, in the living system, or even any more empty place in the central dogma?

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