Term paper

This file describes the term paper project for CSC 450/550. This project is due on the final exam day, Monday, December 16 (in place of a final exam). Please upload a single PDF file containing your term paper on Gradescope by 5:30pm on that date.

The project consists of a paper on a focused topic in bioinformatics of at least 5 pages, single-spaced. The paper should include a bibliography of citations to relevant literature, and any sources that you used.

Let me know your paper topic by Tuesday, November 26, through email or during office hours. A list of possible paper topics (together with relevant sections from the textbook) includes:

• Sequence database searching by BLAST (Sections 5.4-5.5)
• Sequence database searching by QUASAR and BWT-SW (Sections 5.6, 5.8)
• Genome alignment by MUMMER (Sections 4.3-4.4)
• Motif finding by the Gibbs sampler and MEME (Sections 10.3-10.6)
• Genome rearrangements represented by unsigned permutations (Sections 9.3-9.4)
• Evolutionary tree reconstruction (Section 7.3)
• RNA secondary structure prediction (Sections 11.3-11.6)
• Algorithms for interval minimum queries in O(1) time using O(n) time and space preprocessing
• Your own topic? (Please discuss it with me first.)

Your term paper should clearly state the computational problem for your topic, gives its motivation from bioinformatics, describe the computational methods that address the problem, and any known research results. For full marks, your paper needs to go into detail on some aspects of the topic.