Blast

BLAST

Basic Local Alignment Search Tool

Introduction

Blast is the most commonly used database search tool. Since its appearance in 1990, there have been several improvements, most importantly gapped Blast and PSI (Position Specific Iterated) Blast. Other improvements have been in the method used for job queueing at NCBI and in giving different formats for the Blast output. Ongoing developments are PHI (Pattern Hit Initiated) Blast, which combines ProSite-like patterns with Blast searches, and two-sequence Blast.

Blast:

uses a heuristic, local (not global) alignment method.
match scores have a clearly defined statistical interpretation.
- making identifying real matches from random background hits easier.
has an extensive library of references, a manual and a tutorial course.
output can be reprocessed by several other programs (e.g. see MView).
- As the NCBI does not support these programs, format changes to Blast frequently break them.
is best used by following some advice on sequence searching:
- from Steven Brenner
- from Bill Pearson

Blast and Related Programs

Blast at the NCBI and elsewhere
main Blast page	PSI-Blast	PHI-Blast	Two-sequence Blast
WU-Blast at EBI	NCBI-Blast at EBI	Blast-Prints at UCL	GCG Blast Documentation

Results for the WU-Blast search at EBI can be displayed using MView.

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