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)
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
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.