| Topic | Topics | Links & 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).
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| 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".
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|