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
- 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

- 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.