Question: High Scoring Pairs (HSP) in BLAST output
2
gravatar for ramesh.8v
3.9 years ago by
ramesh.8v210
United States
ramesh.8v210 wrote:

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 • 12k views
ADD COMMENTlink modified 3.9 years ago by Denise CS5.1k • written 3.9 years ago by ramesh.8v210
4
gravatar for Pierre Lindenbaum
3.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum129k wrote:

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.

ADD COMMENTlink written 3.9 years ago by Pierre Lindenbaum129k
1

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.

ADD REPLYlink written 3.9 years ago by Soheil Jahangiri10
4
gravatar for Denise CS
3.9 years ago by
Denise CS5.1k
UK, Hinxton, EMBL-EBI
Denise CS5.1k wrote:

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

ADD COMMENTlink written 3.9 years ago by Denise CS5.1k
1
gravatar for Mahmut Uludag
3.9 years ago by
KAUST, Thuwal, Saudi Arabia
Mahmut Uludag20 wrote:

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

ADD COMMENTlink written 3.9 years ago by Mahmut Uludag20
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