Find unique matches then maximum matches

1
Find unique matches then maximum matches
Example A acat B acaa

• Fast building a suffix tree, linear time
  (Ukkonens algorithm)

2
MUMmer

• Approach
• 1. Find MUMs
• 2. Find a longest set of MUMs in the increasing
  order longest increasing subsequence (LIS)
• 3. Close the gaps, identify SNP, large inserts,
  repeats, small mutated regions
• 4. Smith-Waterman to generate alignments between
  MUMs

3
MUMmer

• No need to pre-screen the repetitive regions

• Closely related genomes

• Efficient linear time and space

• Biological features able to identify
• SNP
• Regions of DNA diverged more than SNP
• Repeats in one genome
• Tandem repeats (with difference number of copies)