Wanxing Xu's home page > Course: CS 234, Winter 2008.

CS 234: Computational Methods for the Analysis of Biomolecular Data

Course web page by Prof. Stefano Lonardi.


Topic Generalized Suffix Tree

Use the generalized suffix tree to find the maximal unique matches between two long strings (ideally chromosomes).

Environment JRE 1.5.0 (download page), Eclipse 3.2.2 (download page).
  1. Get background knowledge ... done
  2. Construct suffix tree ... done
  3. Construct generalized suffix tree by multiple strings ... done
  4. Find maximal unique matches ... done
  5. Test and optimize ... done
Demo 9:30, March 18

Paper Presentation

Topic Multiple Sequence Alignment Based on Profile Alignment of Intermediate Sequences, Yue Lu and Sing-Hoi Sze, RECOMB 2007. PDF
Date Time slot #4, March 6, 2008.
Slides CS234_Presentation_Wanxing.pdf