Getting started
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
-     update_blastdb.pl - Download pre-formatted BLAST databases from NCBI
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
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.