Getting started

• Introduction

Search utilities

•     bl2seq - given two sequences in FASTA format, find regions of local similarity
•     blastall - given sequences in FASTA format, find similar sequences in a BLAST database
•     megablast - compare highly similar nucleotide sequences

Advanced utilities

•     blastpgp - create protein profiles with position-specific iterative BLAST, or search protein databases using pattern-hit-initiated BLAST
•     seedtop - search BLAST databases using PROSITE patterns
•     rpsblast - search an RPSBLAST database using the BLAST algorithm
•     blastclust - automatic sequence clustering
•     impala - search an RPSBLAST database using the Smith-Waterman algorithm (deprecated)

Network utilities

•     netblast - perform BLAST searches using the servers and databases at NCBI
•     wwwblast - set up your own BLAST web server
•     web_blast.pl - blast web service interface example

Sequence manipulation utilities

•     fastacmd - retrieve FASTA sequences from BLAST databases
•     formatdb - create BLAST databases from FASTA sequences
•     makemat / copymat - convert a set of profiles into an RPSBLAST database (deprecated)
•     formatrpsdb - create an RPSBLAST database from sequences in Score-matrix-parameters format

Downloads

• Standalone utilities
• BLAST databases
• RPSBLAST databases

Glossary

•     filtering - a process by which low complexity regions are masked from query sequences; see the documentation on filter strings.
•     profile - A position-specific scoring matrix (PSSM) created by position-specific iterated BLAST (psiblast).
•     FASTA - Originally a protein alignment algorithm, in this context FASTA refers to an uncompressed text representation of nucleotide or protein sequence data.
•     BLAST database - A set of protein or nucleotide sequences in a format suitable for efficient searching.
•     RPSBLAST database - A set of profiles in a format suitable for efficient searching.