Sample Midterm Questions for a Takehome Exam

Answer each of the questions in standard written English, or with documentary information as appropriate to the problem. The questions are intended to be answerable within two typewritten pages of text, and most can be answered well with much less text. In general, shorter answers will be preferred over longer answers, but be sure that you address each part of the question.

1. Describe the classical, map-based approach to genome sequencing, and the alternative, ÔrandomÕ approach. What are the main advantages and disadvantages to each approach?

2. Distinguish genomics from genetics. What are the goals of genomics? Give examples of several types of scientific questions that can be addressed more easily with genomic methods.

3. Describe the Smith-Waterman algorithm for pairwise sequence alignment. Illustrate your explanation with an example alignment of two short (<10 AA) sequences.

4. To perform pairwise sequence alignment, we relied on a "BLOSUM50" matrix. What are the desirable properties of this matrix? In other words, what do the numbers in the matrix mean?

5. NCBI provides several "flavors" of BLAST: blastp, blastn, blastx, tblastn, tblastx. What is the difference between these different search algorithms? Provide an example for each of them of circumstances under which it would be the appropriate search tool to use. HINT: this question will be much easier to answer if you are caught up on your readings in the textbook.

6. The sequence below that has been extracted from genbank and modified. The following questions refer to this sequence (sequence#1): What is the identity of this gene? What organism is it from, and what gene does it encode? How has the sequence been modified? Print the original genbank file (it should be just one page), and use a highlighter to identify the bases that have been changed.

Sequence#1: