A high-scoring segment pair, or HSP, is a subsegment of a pair of sequences, either nucleotide or amino acid, that share high level of similarity. The level of similarity between the sequences depends on the settings of the local or global alignment algorithm which generated them. Depending on the sequences, the alignment algorithm, and the settings used, one can find numerous HSPs within a given pair of inputted sequences.
Show how HSPs are generated by alignment algorithms such as BLAST.
Show how HSP Data is generated and displayed in various CoGE applications.
I'm sure references will be needed.