DOKK / manpages / debian 12 / pftools / pfsearchV3.1.en
PFSEARCHV3(1) User Commands PFSEARCHV3(1)

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

pfsearch [options] profile database

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

[-l] : level to use for cutoff
[-m] : mode to use for normalization

[-c] : output indices to given file
[-i] : use indices stored in given file

[-C] : heuristic cutoff value
[-A] : only print heuristic scores to stdout

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

[-a] : only print filter scores to stdout
[-d] : dump passed heuristic and filter sequences

[-s] : enforces SSE 2 only instruction set
[-t] : max number of threads to use
[-T] : max number of threads to use for heuristic phase only. (IO bounds)
[-f] : disable CPU affinity file
[-M] : file containing thread mask, one row for one thread
[-k] : Prevent core resource sharing
[-b] : if both SSE 2 & 4.1 are available, split half-half using linked resources

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

[-v] : verbose on stderr
[-h] : output command help

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

March 2017 pfsearchV3 3