Figure 2.

The five types of sub-alignment region around HSPs in which dynamic programming may be applied. The start of an HSP (A), handling small gaps by joining two adjacent ends of HSPs (B), handling large gaps by joining two distant HSPs via a span (C,D) and the end of an HSP (E). Other features, such as splice sites are incorporated into the alignment within the SARs.

Slater and Birney BMC Bioinformatics 2005 6:31   doi:10.1186/1471-2105-6-31
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