To keep the extracted files/directories in one place, we should create a new subdirectory (folder) under E: (or other directory of your choice), named as blast-2.2.15 (for current release). After moving the saved archive to this newly created subdirectory, we can double click the archive to extract and install the programs. A DOS terminal window will open briefly with file names flashing by during this process. Successful installation creates three subdirectories under blast-2.2.15: bin, data, and doc. The bin subdirectory contains the executable programs (see details in Table 2.1.2).
| Table 2.1.2 BLAST Programs Under the bin Directory | |
| Name | Function |
|---|---|
| bl2seq | Directly aligns two FASTA sequences of the same of different sequence types |
| blastall | Aligns protein/nucleotide queries against different databases based user input (see section 1.1) |
| blastclust | Clusters nucleotide or protein sequences into groups based on similarity |
| blastpgp | Performs iterative protein search with custom position specific matrix (ref) |
| copymat | Copies custom scoremat, one of the old tools needed to generate conserved domain database for rpsblast |
| fastacmd | Dumps out the FASTA sequences from a formatted BLAST database |
| formatdb | Formats FASTA or ASN.1 sequence(s) into a BLAST database |
| formatrpsdb | Format the scoremats into a conserved domain database for rpsblast |
| impala | Searches protein sequences against a conserved domain database |
| makemat | Makes scoremat, one of the two old tools needed to generate a conserved domain database |
| megablast | A faster alternative to traditional blastn |
| rpsblast | Searches a query for presence of known conserved domains |
| seedtop | Searches for presence of given patterns in a database or query sequence |
The documents on individual programs are in the doc subdirectory. Matrices for scoring protein alignments and other files needed by programs, such as Cn3D and Sequin, are in the data subdirectory.
Note that data directory is not for storage of custom databases. For storage of blast databases, we need to create a subdirectory named db under blast-2.2.15.