This was a take-home exam.
BSCI 348s - Bioinformatics in Genomics and Evolution
Answer the following questions in standard written English, or with documentary information as appropriate to the question. Your entire exam should not exceed ten printed pages. Credit will be given for the completeness, accuracy, and efficiency of your answers (in other words, the best score will be received by answers that use relatively few words to provide a clear and complete answer to the question).
1. Describe the field of bioinformatics, and explain why it is an area of increasing importance. Be sure to distinguish genetics from genomics, and identify how bioinformatics is important in genomics. You should also indicate how bioinformatics is distinguished from related fields.
2. Consider genbank, one of the main sequence databases, which is housed and maintained by NCBI. Describe genbank's mission, contrast it with the Swissprot mission, and explain how the structure of genbank's database is designed to meet its mission. Be sure to include some examples of activities that are not within genbank's purview, and explain how this influences the ways in which genbank can be used.
3. What is a PAM matrix, and how are they determined? Your answer should indicate the source of the data that are used to make the matrix, give a qualitative description of the calculations that are used to transform the data, and identify the units of the resulting numbers (i.e., what are the units for a PAM 250 matrix?).
4. Use the Smith-Waterman algorithm to align the following two sequences using a blosum62 scoring matrix:
How would the alignment be different if sequence 1 were truncated to PGSEI?
It is not cheating to use your GCG account at UMBI to check your work, but you should show the full matrix generated by the algorithm. Be sure to make it clear what calculations you performed, as this is necessary for partial credit.
5. Describe the random-clone approach to genome sequencing, and contrast it with the mapped-clone approach. Outline the advantages and disadvantages of each method.