PFSCAN(1)

NAME
pfscan - scan a protein or DNA sequence with a profile library

SYNOPSIS
pfscan [ -abflLrsuxy ] [ seq-file | - ]
            [ profile-library-file | - ] [L=#] [W=#]

DESCRIPTION
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 informations can be specified via the options -a, -l, -L, -r, -u, -s, -x, -y and -z. seq-file contains a sequence in EMBL/SWISS-PROT format (assumed by default) or in Pearson/Fasta format (indicated by option -f). profile-library-file contains a library of profiles in PROSITE format. pfscan can be used as a filter if - is used instead of one of the input filenames.

OPTIONS

-a  Report optimal alignment scores for all profiles regardless of the cut-off value. This option simultaneously forces DISJOINT=UNIQUE.

-b  Search the complementary strand of the DNA sequence as well.

-f  Input sequence is in Pearson/Fasta format.

-l  Indicate highest cut-off level exceeded by the match score in the output list.

-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.

-r  Use raw scores rather than normalized scores for match selection. Normalized scores will not be listed in the output.

-s  List the sequences of the matched regions as well. The output will be a Pearson/Fasta-formatted sequence library.

-u  Forces DISJOINT=UNIQUE.

-x  List profile-sequence alignments in pftools PSA format.

-y  Display alignments between the profile and the matched sequence regions in a human-friendly format.

-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.

PARAMETERS

L=# Cut-off level to be used for match selection. If level L is not specified in the profile, the next higher (if L is negative) or next lower (if L is positive) level specified is used instead.

W=# Output width. Output lines will be truncated after W characters. Default: W=132.

EXAMPLES

(1) 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.

(2) pfscan -by CVPBR322 ecp.prf L=2 Scans both strands of plasmid PBR322 for high-scoring (level 2) E. coli promoter matches. CVPBR322 contains EMBL entry J01749|CVPBR322. ecp.prf contains a profile for E. coli promoters. The output includes profile-sequence alignments in a human-friendly format.

AUTHOR
Philipp Bucher
Philipp.Bucher@isrec.unil.ch