High Scoring Pairs (HSP) in BLAST output

Question

[second_exon]

The term HSP has been used in many research papers while describing BLAST output. What are High Scoring Pairs (HSP)? I'm not very successful in Googling.

Answer 1

[Pierre Lindenbaum]

http://www.ncbi.nlm.nih.gov/books/NBK62051/

A High-scoring Segment Pair (HSP) is a local alignment with no gaps that achieves one of the highest alignment scores in a given search.

[Soheil]

This is odd. I think a HSP can contain gaps. Extension of BLAST seeds might be done by gaps as long as the evalue is less that the user defined value.

Answer 2

[Denise CS]

HSP corresponds to the matching region between the query sequence and the database hit sequence.

Answer 3

[Mahmut Uludag]

Wikipedia BLAST article could be a good read as well; it explains how exact matches are extended to high-scoring segment pairs, how they are evaluated, how alignments are inferred.

https://en.wikipedia.org/wiki/BLAST