Standalone BLAST Incorporates MegaBLAST RPS-BLAST and BLASTClust
With release 2.1.2 NCBIs Standalone BLAST package now contains
three new programs MegaBLAST RPS-BLAST and BLASTClust.
These programs supplement the standard distribution including the
basic BLAST program blastall blastpgp PSI- and PHI-BLAST
bl2seq (a standalone version of BLAST2Sequences) and formatdb (the
program used to create BLAST-ready databases).
MegaBLAST uses an algorithm developed by Webb Miller et al. 
that is designed to swiftly compare two large sets of nucleotide sequences
that differ only slightly from one another perhaps as a result of
sequencing errors. Mega-BLAST is about 10 times faster than BLAST and
is used by NCBI to assemble the clusters that comprise UniGene.
BLASTClust uses a single-linkage clustering process to group protein sequences
based on pairwise matches found using the BLAST algorithm. The program
accepts as input a file of concatenated protein sequences in FASTA format
each with a unique sequence identifer. It returns a file of sequence identifiers
arranged in clusters.
RPS-BLAST uses a protein sequence query to search a library of PSI-BLAST
Position Specific Score Matrices (PSSMs). Also included with the package
are the programs makemat and copymat. These programs
are required to create the RPS-BLAST PSSM libraries. Partially processed
libraries based on the protein domains in the PFAM and SMART databases
are available from NCBI via FTP at ftp://ncbi.nlm.nih.gov/pub/mmdb/cdd/.
In order to calculate more accurate Expect-values BLAST and PSI-BLAST
now take into account the amino acid composition of individual database
sequences. The new Expect-value calculations use a scaling procedure 
that creates a composition-corrected scoring system for each individual
database sequence. Hence identical alignments may receive different
scores depending upon the amino acid composition of the database sequences
involved. An option to generate XML output is also provided (using the
command line option -m 7). Pick up Standalone BLAST 2.1.2
in the executables directory at ftp://ncbi.nlm.nih.gov/blast.
1. Zhang Z S Schwartz L Wagner and
W Miller. J Comput Biol 7:203-14 2000.
2. Altschul SF et al. Nucl Acids Res 25:3389-3402
Schäffer AA et al. Bioinformatics 15:1000-1011