---
name: "pfsearchV2"
section: "1"
platform: "linux"
package: "pftools"
version: "3.2.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pfsearchV2"
---

# pfsearchV2(1)

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

## 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