Man page - pfsearchv3(1)
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Manual
PFSEARCHV3
NAMESYNOPSIS
DESCRIPTION
OPTIONS
Profile
Database
Heuristic
Filter
Optimizations
Printing output
Other
AUTHOR
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.