PFTOOLS
PFTOOLS are algorithms for searching the PROSITE database. There are two tools: PFSCAN and PFSEARCH. PFSCAN compares a protein or nucleic acid sequence against the PROSITE profile library. PFSEARCH compares a query profile against the PROSITE. The result is an unsorted list of profile-sequence matches. A variety of output formats containing different informations can be specified.
The PFTOOLS Algortihms were reported here: Bucher P, Karplus K, Moeri N and Hofmann, K (1996) "A flexible motif search technique based on generalized profiles" Comput. Chem. 20:3-24.
PFSCAN Manual: http://www.isrec.isb-sib.ch/ftp-server/pftools/pft2.3/documentation/pfscan.1.html
PFSEARCH Manual: http://www.isrec.isb-sib.ch/cgi-bin/man.cgi?section=1&topic=pfsearch
INPUT = Nucleic Acid or Protein Sequences (PFSCAN); Nucleic Acid or Protein Profiles (PFSEARCH).
TEST INPUT FILES: PFSCAN
Input file: pfscan_in.txt
TEST OUTPUT FILES
Output file: pfscan_out.txt
TEST INPUT FILES: PFSEARCH
Input file: pfsearch_profile_in.txt
TEST OUTPUT FILES
Output file: align_nuc_out1.txt
