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FASTA

Pearson and Lipman, 1988

pairwise alignment

sequence A        -    -     W    I     V    -    -   

sequence B        -    -     W    I     V    -    -

Fasta looks for a matching region (n=3), then extends the alignment left and right

Step 1. Simple indexing

Step 2. identify match

Step 3. start alignment

faster than dynamic programming, but less sensitive