CS234: Computational Methods for the Analysis of Biomelecular Data


Contact Information

Thanawin Rakthanmanon
rakthant@cs.ucr.edu
Room 368 Eng II


Project

Project Interested: Suffix Arrays

Project Progress
Feb 05, 2010:
Understand the definition of suffix array and its properties.
Also try to understand the common and difference between suffix array and suffix tree.

Feb 16, 2010:
Read paper of J. Karkkainen and P. Sanders, CPM 2003, "Simple Linear Work Suffix Array Construction." [pdf]
Read paper of J. Karkkainen, P. Sanders and S. Burkhardt, Journal of ACM 2006, "Linear Work Suffix Array Construction." [pdf]

Feb 26, 2010:
Read paper of P. Ko and S. Aluru, CPM 2003, "Space efficient linear time construction of suffix arrays." [pdf]
Read paper of S. Zhang and G. Nong, IDC 2008, "Fast and space effieient linear suffix array construction." [pdf]

Mar 1, 2010:
Start implement brute-force version of suffix array
Still try to understand the papers above

Mar 3, 2010:
Read paper of T. Kasai, G. Lee, H. Arimura, S. Arikawa, and K. Park, CPM 2001, "Linear-time longest-common-prefix computation in suffix arrays and its applications." [pdf]

Mar 10, 2010:
Read paper of D. Kim, J. Sim, H. Park, and K. Park, J. Disc. Algor. 2005, "Constructing suffix arrays in linear time." [pdf]