02-714: String Algorithms (Fall 2013)

Tentative Schedule:

TopicTopicsLinks & Reading
1 Exact string matching (Z-algorithm, Knuth-Morris-Pratt, Boyer-Moore, Rabin-Karp)
2 Advanced inexact matching (edit distance, alignment in linear space, Four-Russians' speedup, approximation algorithms for MSA, whole genome alignment)
3 Suffix trees and arrays and their applications; Ukkonen's suffix tree construction algorithm; Burrows-Wheeler transform.
4 Multiple sequence alignment; motif finding; multiple patterns.
5 Compressed self-indices (data structures that support fast searching and complete reconstruction of the full text in sublinear space).
7 Hashing / randomization techniques for big data
  • Locality sensitive hashing
  • Nearest neighbor search for locality sensitive hashing
  • Random projection for motif finding
  • Bloom filters
8 Current research in "Big Genomics".