NAME

       pfsearch - search protein and DNA generalized profiles (legacy)

SYNOPSIS

       pfsearch  [  -abCdfhlLmMkrsuvWxyz  ]  [  profile-file  |  -  ]  [ seq-library-file | - ] [
       parameters ]

DESCRIPTION

       Build protein and DNA generalized profiles and use them to scan and align  sequences,  and
       search databases.

OPTIONS

       -a: report optimal alignment for all sequences.

       -b: search complementary strand of DNA sequences.

       -f: input sequence file is in FASTA format.

       -h: print usage help text.

       -l: indicate highest cut-off level (number).

       -L: indicate highest cut-off level (text).

       -m: report individual matches for circular profiles.

       -r: use raw score.

       -u: force profile disjointness to UNIQUE.

       -C<value>:

              cut-off value. An integer value forces -r. Same as parameter C.

       -M<value>:

              set the normalization mode to use for the score computation.  Overrides the profile
              PRIORITY parameter.

              output modifiers:

       -d: impose length limit on sequence description.

       -k: output using the xPSA header (using keyword=value pairs).

       -s: list sequences of the matched regions.

       -v: suppress warnings on stderr.

       -x: list alignments in PSA format.

       -y: list alignments in human readable form.

       -z: indicate profile start and stop positions.

       -W<value>:

              specifies the output width. Same as parameter W.

              valid (but deprecated) parameters are:

       [C=cut-off-value]
              use option -C instead

       [W=output-width]
              use option -W instead

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used  for
       any other usage of the program.