Special Topics in CS: Bioinformatics
Homework 5  


Pairwise Alignment


The goal of this homework assignment is to give students experience with several pairwise sequence alignment tools. The EMBL-EBI web site has a web-based implementation of several Pairwise Alignment algorithms. These are available at the EMBL-EBI website. Use these tools to answer the following questions. Make sure that you ask for a "printer friendly view" before printing the results. Note that when it asks for a sequence you can paste the entire FASTA formatted sequence into the area for the sequence including the documentation line. This will provide annotation on your printouts that lets you identify the proteins in the alignment.

  • Align bovine insulin precursor (P01317) and human insulin precursor (P01308) using global alignment and the default settings. Submit a printout of the resulting alignment. Give a short description (2-3 sentences) of the characteristics of the alignment produced.
  • Reduce the gap open penalty to 1.0 and repeat the alignment. Submit a printout of the resulting alignment. Do you see any differences? If so, describe them.
  • Repeat #1 using local alignment. Submit a printout of the resulting alignment. Do you see any differences with the global alignment? If so, describe them.
  • Perform a global alignment of the human hemoglobin beta chain (P02023) with the hemocyanin A chain from the American tarantula (P14750). Both of these molecules are globins. Submit a printout of the resulting alignment. Give a short description (2-3 sentences) of the characteristics of the alignment produced.
  • Perform a local alignment of the globin molecules above using the default settings. Submit a printout of the resulting alignment and give a short description of the alignment produced. How does this alignment differ from the global alignment? Which is more appropriate in this case and why?
  • Use the information presented in the handout in class about amino acid substitution matrices and determine an appropriate matrix for the local alignment of the two globins. Which amino acid substitution matrix did you select and why? Perform the local alignment again and compare to your previous results (unless you decided that Blosum62 is the most appropriate.) Submit a printout of this alignment.

    Due: Thursday, Sept. 23, 2004 Submit a hard copy of your answers to the above questions in class on Thursday, Sept. 23, 2004. You do not need to use a special template or to provide references and citations for this homework.