.\"
.\" $Id: pfsearch.1,v 1.4 2003/07/24 08:40:52 vflegel Exp $
.\" Copyright (c) 2003 SIB Swiss Institute of Bioinformatics <pftools@sib.swiss>
.\" Process this file with
.\" groff -man -Tascii <name>
.\" for ascii output or
.\" groff -man -Tps <name>
.\" for postscript output
.\"
.TH PFSEARCH 1 "July 2003" "pftools 2.3" "pftools"
.\" ------------------------------------------------
.\" Name section
.\" ------------------------------------------------
.SH NAME
pfsearch \- search a protein or DNA sequence library for sequence segments 
matching a profile
.\" ------------------------------------------------
.\" Synopsis section
.\" ------------------------------------------------
.SH SYNOPSIS
.TP 10
.B pfsearch
[
.B \-abdfhlLmruksvxyz
] [
.B \-C
.I cut_off
] [
.B \-M
.I mode_nb
] [
.B \-W
.I width
] [
.I profile
|
.B \-
] [
.I sequence_library
|
.B \-
] [
.I parameters
]
.\" ------------------------------------------------
.\" Description section
.\" ------------------------------------------------
.SH DESCRIPTION
.B pfsearch 
compares a query profile against a DNA or protein sequence 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 
.BR \-l , \ \-L , \ \-r , \ \-k , \ \-s , \ \-x , \ \-y
and 
.BR \-z .
The file
.RI ' profile '
contains a profile in
.SM PROSITE
format. The
.RI ' sequence_library '
file contains a sequence library in
.SM EMBL/SWISS-PROT
format (assumed by default) or in Pearson/Fasta
format (indicated by option 
.BR \-f ). 
If
.RB ' \- '
is specified instead of one of the filenames, the corresponding data is read
from the standard input.
.\" ------------------------------------------------
.\" Options section
.\" ------------------------------------------------
.SH OPTIONS 
.\" --- profile ---
.TP
.I profile
Input query profile.
.br
The
.SM PROSITE
profile contained in this file will be used to search for profile to sequence
matches in a biological sequence library. If the filename is replaced by a
.RB ' \- ',
.B pfsearch
will read the profile from
.BR stdin .
.\" --- sequence_library ---
.TP
.I sequence_library
Library of DNA or protein sequences.
.br
This file should contain one or several
.SM EMBL/SWISS-PROT
(default) or Pearson/Fasta (option
.BR \-f )
formatted DNA or protein sequences. The program
.B pfsearch
tries to identify matches between the input profile and all individual
sequences of this library. If the filename is replaced by a
.RB ' \- ',
.B pfsearch
will read the sequence library from
.BR stdin .
.\" --- a ---
.TP
.B \-a
Report optimal alignment scores for 
all sequences regardless of the cut-off value. 
This option simultaneously forces 
.IR DISJOINT = UNIQUE .   
.\" --- b ---
.TP
.B \-b
Search the complementary strands of DNA sequences as well.
.\" --- f ---
.TP
.B \-f
Input sequence library is in Pearson/Fasta format.
.\" --- h ---
.TP
.B \-h
Display usage help text.
.\" --- l ---
.TP
.B \-l
Indicate the value of the highest cut-off level exceeded by the match score
in the output list. 
.\" --- L ---
.TP
.B \-L
Indicate by character string the highest cut-off level exceeded by the match score
in the output list.
.br
.RS
.TP
Note:
The generalized profile format includes a text
string field to specify a name for a cut-off level. The
.B \-L
option causes the program to display the first two characters of this text string
(usually something like
.RI ' ! ',\ ' ? ',\ ' ?? ',
etc.) at the beginning of each match description.
.RE
.\" --- m ---
.TP
.B \-m
Report individual matches for circular profiles.
.br
If the profile is circular, each match between a sequence and a profile can be composed
of a stretch of individual matches of the profile. By default,
.B pfsearch
reports only the total matched region. When this option is set, detailed information for 
each individual match will be output as well.
.RS
.TP
Note:
The scoring system for most circular profiles has been optimized to find
total matches, therefore the normalized scores of individual matches of a circular profile
to a sequence should be considered with caution.
.RE
.\" --- r ---
.TP
.B \-r
Use raw scores rather than normalized 
scores for match selection. The normalized score is not printed, this option is useful
to create raw score lists to be used with
.BR pfscale (1).
.\" --- u ---
.TP
.B \-u
Forces
.IR DISJOINT = UNIQUE . 
.\" --- C ---
.TP
.BI \-C\  cut_off
Cut-off value to be used for match selection.
.br
The value of
.RI ' cut_off '
overwrites the level zero cut-off value specified in the profile.
.br
An integer argument is interpreted as a raw score value,
a decimal argument as a normalized score value.
.br
Default: profile level 0 cut-off value (normalized score if present)
.RS
.TP
Note:
Compared to release 2.2, an integer value does
.I not
force option
.BR \-r .
Normalized scores will still be listed in output if an integer cut-off
is specified on the command line but cut-off level computation will be
based on raw score.
.RE
.\" --- M ---
.TP
.BI \-M\  mode_nb
Normalization mode to use for score computation.
.br
The
.RI ' mode_nb '
specifies which normalization mode defined in the profile should be used
to compute the normalized scores for profile to sequence matches. This
option will override the profile's
.I PRIORITY
parameter.
.br
If the specified normalization mode does not exist in the profile, an error
message will be output to standard error and the search is interrupted.
.br
Type: integer
.br
Default: lowest priority mode defined in the profile
.\" ------------------------------------------------
.\" Output modifiers subsection
.\" ------------------------------------------------
.SS Output modifiers
.\" --- d ---
.TP
.B \-d
Limit sequence description length.
.br
If this option is set, the description of the sequence on the header line
will be limited in length. If the match information is longer than
the output width specified using option
.BR \-W ,
the sequence description will not be printed. Else the description will be truncated
to fit the
.B \-W
value.
.br
By default, the sequence description is not truncated. This option can not be used
when option
.B \-k
is set.
.\" --- k ---
.TP
.B \-k
Use
.BR xpsa (5)
headers for output.
.br
When this option is set, all output types 
.RI ( see
below) will use
an
.BR xpsa (5)
style header line. This format uses
.IR keyword = value
pairs to output alignment parameters. It is useful to transfer information between
different sequence alignment tools.
.\" --- s ---
.TP
.B \-s
List the sequences of the matched regions as well. 
The output will be a Pearson/Fasta-formatted sequence
library.
.\" --- v ---
.TP
.B \-v
Suppress sequence/profile parsing warnings.
If this option is set no warning messages will be printed on
.IR stderr .
Only fatal errors will be reported. This option should be used
with caution.
.\" --- x ---
.TP
.B \-x
List profile-sequence alignments 
in
.BR psa (5)
format. Please refer to the corresponding man page for more information. 
.\" --- y ---
.TP
.B \-y
Display alignments between the profile and the matched sequence regions in 
a human-friendly pairwise alignment format.   
.\" --- z ---
.TP
.B \-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.
.\" --- W ---
.TP
.BI \-W\  width
Set alignment output width.
.br
The value of
.RI ' width '
specifies how many residues will be output on one line when any of the
.BR \-s ,\  \-x \ or\  \-y
options is set.
.br
Type: integer
.br
Default: 60
.\" ------------------------------------------------
.\" Parameters section
.\" ------------------------------------------------
.SH PARAMETERS 
.TP
Note:
for backwards compatibility, release 2.3 of the
.B pftools
package will parse the version 2.2 style parameters, but these are
.I deprecated
and the corresponding option (refer to the
.I options
section) should be used instead.
.TP
C=#
Cut-off value.
.br
Use option
.B \-C
instead.
.TP
W=#
Output width. 
.br
Use option
.B \-W
instead.
.\" ------------------------------------------------
.\" Examples section
.\" ------------------------------------------------
.SH EXAMPLES 
.TP
(1)
.B pfsearch
\-f \-C 6.0 sh3.prf sh3.seq
.IP
Searches the Pearson/Fasta-formatted protein sequence library
.RI ' sh3.seq '
for SH3 domains with a cut-off value of 6.0 normalized score units.
The file
.RI ' sh3.seq '
contains 20 SH3 domain-containing protein sequences from
.SM SWISS-PROT
release 32.
The file
.RI ' sh3.prf '
contains the
.SM PROSITE
entry SH3/PS50002.
.TP
(2)
.B pfsearch
\-bx ecp.prf CVPBR322 |
.B psa2msa   
\-du |    
.B readseq
\-p -fMSF > ecp.msf
.IP
Generates a multiple sequence alignment  of potential
.I E. coli
promoters on both strands of plasmid pBR322.
The file
.RI ' ecp.prf ' 
contains a profile for
.I E. coli   
promoters.  
The file
.RI ' CVPBR322 '
 contains
.SM EMBL
entry J01749|CVPBR322.
The result file
.RI ' ecp.msf '
can further be processed by
.SM GCG
programs accepting MSF files as input.
.\" ------------------------------------------------
.\" Exit code section
.\" ------------------------------------------------
.SH EXIT CODE
.LP
On successful completion of its task,
.B pfsearch
will return an exit code of 0. If an error occurs, a diagnostic message will be
output on standard error and the exit code will be different from 0. When conflicting
options where passed to the program but the task could nevertheless be completed, warnings
will be issued on standard error.
.\" ------------------------------------------------
.\" Bugs section
.\" ------------------------------------------------
.SH "BUGS"
The use of normalized scores as cut-off values can lead to a different behaviour when compared
to raw scores. This is due to the inherent rounding inaccuracy of real numbers.
The normalized scores used as cut-offs should be rounded down in order to circumvent this 
problem.
.\" ------------------------------------------------
.\" See also section
.\" ------------------------------------------------
.SH "SEE ALSO"
.BR pfscan (1),
.BR pfmake (1),
.BR psa2msa (1),
.BR psa (5),
.BR xpsa (5)
.\" ------------------------------------------------
.\" Author section
.\" ------------------------------------------------
.SH AUTHOR
The
.B pftools
package was developed by Philipp Bucher.
.br
Any comments or suggestions should be addressed to <pftools@sib.swiss>.