General View of How the BLAST Program Works (see also lecture No. 3):

• BLAST - The program compares the query to each sequence in database using heuristic rules to speed up the pairwise comparison. It first creates sequence abstraction by listing exact and similar words This is done in advance for each sequence in the database on the run for a certain query. BLAST finds similar words between the query and each database sequence. It then extends such words to obtain high-scoring sequence pairs (HSPs). It also calculates statistics analytically like FastA does.
  BLAST 2.0 is a new version with new capabilities such as Gapped-Blast and PSI-Blast.
• GAPPED BLAST - This algorithm allows gaps to be introduced into the alignments. That means that similar regions are not broken into several segments (as in the older versions). This method reflects biological relationships much better than ordinary Blast.
• PSI - BLAST - (Position Specific Iterated ) Blast provides a new automatic "profile like" search. The program first performs a gapped blast search of the database. The information of the significant alignments are then used by the program to construct a position specific (PS) score matrix. This matrix replaces the query sequence in the next round of database searching. The program may be iterated until no new significant alignments are found.