.TH PFSCAN  1 "June 1999" "pftools 2.2"
.SH NAME
pfscan \- scan a protein or DNA sequence with a profile library 

.SH SYNOPSIS
.B pfscan
[ -abflLrsuxy ] [ seq-file | - ]
            [ profile-library-file | - ]    [L=#] [W=#]
.SH DESCRIPTION
.B pfscan 
compares a protein or nucleic acid sequence against a profile library. 
The result is an unsorted list of profile-sequence matches written to
the standard output.
A variety of output formats containing different information can be specified
via the options
.I -a, -l, -L, -r, -u, -s, -x, -y
and 
.I -z.
.I seq-file
contains a sequence in EMBL/SWISS-PROT
format (assumed by default) or in Pearson/Fasta
format (indicated by option 
.I -f).
.I profile-library-file 
contains a library of profiles in PROSITE format. 
.B pfscan
can be used as a filter if - is used instead of one of the input
filenames.
.SH OPTIONS 
.TP
\-a
Report optimal alignment scores for 
all profiles regardless of the cut-off value. 
This option simultaneously forces DISJOINT=UNIQUE.   
.TP
\-b
Search the complementary strand of the DNA sequence as well.
.TP
\-f
Input sequence is in Pearson/Fasta format.
.TP
\-l
Indicate highest cut-off level exceeded by the match score
in the output list. 
.TP
\-L
Indicate by character string the highest cut-off level exceeded by the match score
in the output list. Note that the generalized profile format includes a text
string field to specify a name for a cut-off level. The \-L option causes the
program to display the first two characters of this text string
(usually something like "!" "?", "??", etc.) at the beginning of each match description.
.TP
\-r
Use raw scores rather than normalized 
scores for match selection. Normalized scores 
will not be listed in the output. 
.TP
\-s
List the sequences of the matched regions as well. 
The output will be a Pearson/Fasta-formatted sequence
library.
.TP
\-u
Forces DISJOINT=UNIQUE. 
.TP
\-x
List profile-sequence alignments 
in pftools PSA format.  
.TP
\-y
Display alignments between the profile and the matched sequence regions in 
a human-friendly format.   
.TP
\-z
Indicate starting and ending position of the matched profile range. The latter
position will be given as a negative offset from the end of the profile. Thus
the range [    1,    -1] means entire profile.
.SH PARAMETERS
.TP
L=#
Cut-off level to be used for match selection.
If level 
.I L
is not specified in the profile, the next higher (if 
.I L
is negative) or next lower (if
.I L
is positive) level specified
is used instead.
.TP
W=#
Output width.
Output lines will be truncated after
.I W
characters.
Default: W=132.
.SH EXAMPLES
.TP
(1)
.B pfscan
-s GTPA_HUMAN prosite13.prf

Scans the human GAP protein for matches to profiles in PROSITE 
release 13. 
GTPA_HUMAN contains the SWISS-PROT entry P20936|GTPA_HUMAN.
prosite13.prf contains all profile entries of PROSITE release 13.  
The output is a Pearson/Fasta-formatted sequence library containing 
all sequence regions of the input sequence matching a profile in the 
profile library. 
.TP
(2)
.B pfscan
-by CVPBR322 ecp.prf L=2

Scans both strands of plasmid PBR322 for high-scoring (level 2) 
.I E. coli
promoter matches.   
CVPBR322 contains EMBL entry J01749|CVPBR322.
ecp.prf contains a profile for
.I E. coli  
promoters.
The output includes profile-sequence alignments in a human-friendly
format. 
.SH AUTHOR
Philipp Bucher
.br
Philipp.Bucher@isrec.unil.ch