---
name: "pfsearchV3"
section: "1"
platform: "linux"
package: "pftools"
version: "3.2.12-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pfsearchV3"
---

# pfsearchV3(1)

search protein and DNA generalized profiles (version 3)

## NAME

pfsearchV3 - search protein and DNA generalized profiles (version 3)

## SYNOPSIS

**pfsearch** \[options\] profile database

## DESCRIPTION

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

## OPTIONS

### Profile

- **--level**

  \[-l\] : level to use for cutoff

- **--mode**

  \[-m\] : mode to use for normalization

### Database

- **--create-index-database**

  \[-c\] : output indices to given file

- **--use-index-database**

  \[-i\] : use indices stored in given file

### Heuristic

- **--cutoff**

  \[-C\] : heuristic cutoff value

- **--dump-heuristic-scores**

  \[-A\] : only print heuristic scores to stdout

**--dump-heuristic-sequences** \[-D\] : dump passed heuristic sequences

### Filter

- **--dump-filter-scores**

  \[-a\] : only print filter scores to stdout

- **--dump-filter-sequences**

  \[-d\] : dump passed heuristic and filter sequences

### Optimizations

- **--sse2**

  \[-s\] : enforces SSE 2 only instruction set

- **--nthreads**

  \[-t\] : max number of threads to use

- **--max-heuristic-nthreads**

  \[-T\] : max number of threads to use for heuristic phase only. (IO bounds)

- **--no-affinity**

  \[-f\] : disable CPU affinity file

- **--thread-affinity**

  \[-M\] : file containing thread mask, one row for one thread

- **--no-shared-core**

  \[-k\] : Prevent core resource sharing

- **--split**

  \[-b\] : if both SSE 2 & 4.1 are available, split half-half using linked resources

### Printing output

- **--output-method**

  \[-o\] : printing output method

-

  \== 0 replicates the pfseach output without options (DEFAULT)

-

  \== 1 simple output

-

  \== 2 replicates pfsearch **-lxz** output

-

  \== 3 replicates pfscan **-lxz** output

-

  \== 4 tsv output (single line tab delimited)

- **--output-length**

  \[-W\] : maximum number of column for sequence output printing

### Other

- **--verbose**

  \[-v\] : verbose on stderr

- **--help**

  \[-h\] : output command help

## AUTHOR

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