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High Scoring Pairs (HSP) in BLAST output

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.

blast
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updated by Denise CS Denise CS • written by second_exon second_exon

3 answers

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.

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written by Pierre Lindenbaum Pierre Lindenbaum

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.

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written by Soheil • Soheil

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

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written by Denise CS Denise CS

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

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written by Mahmut Uludag • Mahmut Uludag

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