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hmmemit(1)			 HMMER Manual			    hmmemit(1)

NAME
       hmmemit - sample	sequences from a profile

SYNOPSIS
       hmmemit [options] hmmfile

DESCRIPTION
       The  hmmemit  program samples (emits) sequences from the	profile	HMM(s)
       in hmmfile, and writes them to output.  Sampling	sequences may be  use-
       ful  for	a variety of purposes, including creating synthetic true posi-
       tives for benchmarks or tests.

       The default is to sample	one unaligned sequence from the	core probabil-
       ity model, which	means that each	sequence consists of  one  full-length
       domain.	 Alternatively,	 with the -c option, you can emit a simple ma-
       jority-rule consensus sequence; or with the -a option, you can emit  an
       alignment (in which case, you probably also want	to set -N to something
       other than its default of 1 sequence per	model).

       As  another option, with	the -p option you can sample a sequence	from a
       fully configured	HMMER search profile. This means sampling  a  `homolo-
       gous  sequence' by HMMER's definition, including	nonhomologous flanking
       sequences, local	alignments, and	multiple domains per sequence, depend-
       ing on the length model and alignment mode chosen for the profile.

       The hmmfile may contain a library of HMMs, in which case	each HMM  will
       be used in turn.

       hmmfile	may  be	 '-' (dash), which means reading this input from stdin
       rather than a file.

COMMON OPTIONS
       -h     Help; print a brief reminder  of	command	 line  usage  and  all
	      available	options.

       -o <f> Direct the output	sequences to file <f>, rather than to stdout.

       -N <n> Sample <n> sequences per model, rather than just one.

OPTIONS	CONTROLLING WHAT TO EMIT
       The  default  is	 to  sample  N sequences from the core model. Alterna-
       tively, you may choose one (and only one)  of  the  following  alterna-
       tives.

       -a     Emit  an	alignment for each HMM in the hmmfile rather than sam-
	      pling unaligned sequences	one at a time.

       -c     Emit a plurality-rule consensus sequence,	instead	of sampling  a
	      sequence	from  the  profile HMM's probability distribution. The
	      consensus	sequence is formed by selecting	the maximum  probabil-
	      ity residue at each match	state.

       -C     Emit a fancier plurality-rule consensus sequence than the	-c op-
	      tion. If the maximum probability residue has p < minl show it as
	      a	 lower	case  'any'  residue (n	or x); if p >= minl and	< minu
	      show it as a lower case residue; and if p	>= minu	show it	as  an
	      upper  case  residue.  The default settings of minu and minl are
	      both 0.0,	which means -C gives the same output as	-c unless  you
	      also set minu and	minl to	what you want.

       -p     Sample unaligned sequences from the implicit search profile, not
	      from the core model.  The	core model consists only of the	homol-
	      ogous  states (between the begin and end states of a HMMER Plan7
	      model). The profile includes  the	 nonhomologous	N,  C,	and  J
	      states,  local/glocal  and uni/multihit algorithm	configuration,
	      and the target length model.  Therefore sequences	sampled	from a
	      profile may include nonhomologous	 as  well  as  homologous  se-
	      quences,	and may	contain	more than one homologous sequence seg-
	      ment. By default,	the profile is in multihit local mode, and the
	      target sequence length is	configured for L=400.

OPTIONS	CONTROLLING EMISSION FROM PROFILES
       These options require that you have set the -p option.

       -L <n> Configure	the profile's target sequence length model to generate
	      a	mean length of approximately <n> rather	than  the  default  of
	      400.

       --local
	      Configure	the profile for	multihit local alignment.

       --unilocal
	      Configure	 the  profile for unihit local alignment (Smith/Water-
	      man).

       --glocal
	      Configure	the profile for	multihit glocal	alignment.

       --uniglocal
	      Configure	the profile for	unihit glocal alignment.

OPTIONS	CONTROLLING FANCY CONSENSUS EMISSION
       These options require that you have set the -C option.

       --minl <x>
	      Sets the minl threshold for showing weakly conserved residues as
	      lower case.  (0 <= x <= 1)

       --minu <x>
	      Sets the minu threshold for showing strongly conserved  residues
	      as upper case.  (0 <= x <= 1)

OTHER OPTIONS
       --seed <n>
	      Seed  the	random number generator	with <n>, an integer >=	0.  If
	      <n> is nonzero, any stochastic simulations will be reproducible;
	      the same command will give the same results.  If <n> is  0,  the
	      random  number  generator	 is seeded arbitrarily,	and stochastic
	      simulations will vary from run to	run of the same	command.   The
	      default  is  0: use an arbitrary seed, so	different hmmemit runs
	      will generate different samples.

SEE ALSO
       See hmmer(1) for	a master man page with a list of  all  the  individual
       man pages for programs in the HMMER package.

       For  complete documentation, see	the user guide that came with your HM-
       MER distribution	(Userguide.pdf); or see	the HMMER web page (http://hm-
       mer.org/).

COPYRIGHT
       Copyright (C) 2023 Howard Hughes	Medical	Institute.
       Freely distributed under	the BSD	open source license.

       For additional information on copyright and  licensing,	see  the  file
       called  COPYRIGHT  in  your HMMER source	distribution, or see the HMMER
       web page	(http://hmmer.org/).

AUTHOR
       http://eddylab.org

HMMER 3.4			   Aug 2023			    hmmemit(1)

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