NAME

       pfsearchV2  -  search  a  protein or DNA sequence library for sequence segments matching a
       profile

SYNOPSIS

       pfsearchV2 [ -abflLrsuxyz ] [ profile-file | - ]
                   [ seq-library-file | - ]    [C=#] [W=#]

DESCRIPTION

       pfsearchV2 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  -a,
       -l, -L, -r, -u, -s, -x, -y, -z, and the command-line parameter C=#.  profile-file contains
       a profile in PROSITE format.  seq-library-file contains a sequence library in  EMBL/SWISS-
       PROT  format  (assumed  by  default)  or in Pearson/Fasta format (indicated by option -f).
       pfsearchV2 can be used as a filter if - is used instead of one of the input filenames.

OPTIONS

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

       -b     Search the complementary strands of DNA sequences as well.

       -f     Input sequence-library is in Pearson/Fasta format.

       -l     Indicate  by  number  the  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

       C=#    Cut-off  value.  Over-writes the level zero cut-off value specified in the profile.
              An integer argument is interpreted as a raw score value, a decimal  argument  as  a
              normalized score value. An integer value forces option -r.

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

EXAMPLES

       (1)    pfsearchV2 -f sh3.prf sh3.seq C=6.0

              Searches  the  Pearson/Fasta-formatted  protein  sequence  library  sh3.seq for SH3
              domains with a cut-off value of 6.0 normalized score units.   sh3.seq  contains  20
              SH3  domain-containing  protein  sequences  from  SWISS-PROT  release  32.  sh3.prf
              contains the PROSITE entry SH3/PS50002.

       (2)    pfsearchV2 -bx ecp.prf CVPBR322 | psa2msa -du | readseq -p -fMSF > ecp.msf

              Generates a multiple sequence alignment  of potential E.  coli  promoters  on  both
              strands  of  plasmid  pBR322.   ecp.prf  contains  a profile for E. coli promoters.
              CVPBR322 contains EMBL entry J01749|CVPBR322.  The result file ecp.msf can  further
              be processed by GCG programs accepting MSF files as input.

              See also manual pages of psa2msa.

AUTHOR

       Philipp Bucher
       Philipp.Bucher@isrec.unil.ch