Fig. 10
From: Split-alignment of genomes finds orthologies more accurately
The split-alignment algorithm. Left: input to the algorithm, two local alignments that overlap in the query (top, human) sequence. Right: algorithm layout. This example uses match score=1, mismatch cost=1, and gap cost=2+1 ×gap length. Match, mismatch, and insertion scores (A i j ) are written beneath each letter, whereas deletion scores (D ij ) are written between letters. The red lines show the optimal split-alignment