PFSEARCHV3

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.