RPSBLAST
RPSBLAST (Reverse PSIBLAST) performs a blast search of a protein sequence against a database of profiles: domains that are associated with particular families of proteins. RPSBLAST is the opposite of PSIBLAST that searches a profile against a database of sequences, hence the 'Reverse'. The submitted sequence is compared to the consensus sequences for many families of proteins. The tool is useful for identifying which family your protein belongs to, especially over larger domains. This program is a companion to BLIMPS, which identifies specific blocks or domains in a more localized way.
RPS-BLAST uses a BLAST-like algorithm, finding single- or double-word hits and then performing an ungapped extension on these candidate matches. If a sufficiently high-scoring ungapped alignment is produced, a gapped extension is performed and those (gapped) alignments with sufficiently low expect value are reported. This procedure is in contrast to IMPALA that performs a Smith-Waterman calculation between the query and each profile, rather than using a word-hit approach to identify matches that should be extended. RPS-BLAST was coded by Sergei Shavirin with some help from Tom Madden.
Manual: http://www.ncbi.nlm.nih.gov/blast/docs/rpsblast.html
INPUT = Protein or Nucleic Acid Sequences.
TEST INPUT FILES
Input file: rpsblast_in.txt
TEST OUTPUT FILES
Output file: rpsblast_out.txt (query against PFAM database)