BLAST - Basic Local Alignment Search Tool

Blast programs use a heuristic search algorithm. The programs use the statistical methods of Karlin and Altschul [2]. BLAST programs were designed for fast database searching, with minimal sacrifice of sensitivity for distantly related sequences. The programs search databases in a special compressed format. To use your own private database with BlAST, you need to convert it to the BLAST format. Direct pointer: The BLAST at NCBI: [16] It also can be run through one of the retrieval systems (recommended). For example: GeneWeb mirror site at Weizmann Institute: [7]

BLAST is a family of programs, following is a table of the BALST variants:

  

Figure 5.5: Variants of BLAST family

The BLAST 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( Also called advanced BLAST). It can perform gapped alignments) such as Gapped-BLST and PSI-BLAST (detail below). The GAPPED BLAST 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.

Blast interfaces like www.ncbi.nlm.nih.gov/BLAST can be used to run BLAST of a chosen query against the NCBI databases .