The High-scoring Segment Pair (HSP) is the fundamental unit 
     of BLAST algorithm output.  An HSP consists of two sequence
     fragments of arbitrary but equal length whose  alignment  is
     locally  maximal  and for which the alignment score meets or
     exceeds a threshold or cutoff score.  A set of HSPs is  thus
     defined  by  two  sequences,  a scoring system, and a cutoff
     score; this set may be empty if the cutoff score  is  suffi-
     ciently  high.   In  the programmatic implementations of the
     BLAST algorithm described here, each HSP consists of a  seg-
     ment  from  the  query  sequence  and  one  from  a database
     sequence.  The sensitivity and speed of the programs can  be
     adjusted  via  the standard BLAST algorithm parameters W, T,
     and X (Altschul et al., 1990); selectivity of  the  programs
     can be adjusted via the cutoff score.

Presented by Fredj Tekaia tekaia@pasteur.fr