Figure 1.

Exclusion of low-scoring regions from alignment fragments. The scoring scheme used in DIALIGN gives relatively high weight scores to single fragments with high Needleman-Wunsch scores (a). In our new approach, we exclude low-scoring sub-regions within long fragments by applying a stop criterion for fragment extension. This can result in the replacement of a long fragment f by multiple sub-fragments (b) or in a completely different alignment (c).