makemat / copymat - convert a set of profiles into an
RPSBLAST database
rpsblast - search
an RPSBLAST database using the BLAST algorithm
formatrpsdb - create
an RPSBLAST database from sequences in Score-matrix-parameters format
impala - search an
RPSBLAST database using the Smith-Waterman algorithm (deprecated)
Glossary
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.