1. Genome alignment
Usman Roshan

2. Applications Genome sequencing on the rise
Whole genome comparison provides a deeper understanding of biology
Evolutionary history
Non-coding regions
Variant detection

3. Methods General two-fold approach
1. Find high scoring segments between pair of genomes.
Similar to BLAST like k-mer search using hash-tables
Also done with suffix tree
Similar to short read mapping strategies
2. Perform constrained alignment between high scoring segments

4. Longest increasing subsequence
Simple algorithm takes O(n2) time where n is the input size (total numbers in sequence)
Can be solved in O(nlog(n)) time by creating extra data structures and remembering where the previous longest subsequence ended

5. Simple genome alignment
Find high scoring segments with hash tables
Line up high scoring segments and find longest increasing subsequence (like in MUMmer)
Align between the segments
Output full genome alignment

6. Programs and experimental comparison
Alignathon

7. Exact methods
What if we used Smith-Waterman or another exact method to find high scoring segments?
Results on simulated data