Ubuntu Manpage: nhmmer - search DNA/RNA queries against a DNA/RNA sequence database

NAME

       nhmmer - search DNA/RNA queries against a DNA/RNA sequence database

SYNOPSIS

       nhmmer [options] <queryfile> <seqdb>

DESCRIPTION

       nhmmer  is  used  to  search  one or more nucleotide queries against a nucleotide sequence
       database.  For each query in <queryfile>, use that query to search the target database  of
       sequences  in  <seqdb>,  and  output  a  ranked list of the hits with the most significant
       matches to the query. A query may be either  a  profile  model  built  using  hmmbuild,  a
       sequence  alignment,  or  a  single sequence. Sequence based queries can be in a number of
       formats (see --qformat), and can typically  be  autodetected.  Note  that  only  Stockholm
       format supports the use of multiple sequence-based queries.

       Either the query <queryfile> or the target <seqdb> may be '-' (a dash character), in which
       case the query file or target database input will be read from a <stdin> pipe  instead  of
       from  a  file.  Only one input source can come through <stdin>, not both.  If the query is
       sequence-based and  passed  via  <stdin>,  the  --qformat  flag  must  be  used.   If  the
       <queryfile>  contains  more than one query, then <seqdb> cannot come from <stdin>, because
       we can't rewind the streaming target database to search it with another profile.

       If the query is sequence-based, and not from <stdin>, a new  file  containing  the  HMM(s)
       built  from  the input(s) in <queryfile> may optionally be produced, with the filename set
       using the --hmmout flag.

       The output format is designed to be  human-readable,  but  is  often  so  voluminous  that
       reading it is impractical, and parsing it is a pain. The --tblout option saves output in a
       simple tabular format that  is  concise  and  easier  to  parse.   The  -o  option  allows
       redirecting the main output, including throwing it away in /dev/null.

OPTIONS

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

OPTIONS FOR CONTROLLING OUTPUT

       -o <f> Direct the main human-readable output to a file <f> instead of the default stdout.

       -A <f> Save  a  multiple  alignment  of  all  significant hits (those satisfying inclusion
              thresholds) to the file <f>.

       --tblout <f>
              Save a simple tabular (space-delimited) file  summarizing  the  per-target  output,
              with one data line per homologous target sequence found.

       --dfamtblout <f>
              Save  a  tabular  (space-delimited) file summarizing the per-hit output, similar to
              --tblout but more succinct.

       --aliscoresout <f>
              Save to file a list of per-position scores for  each  hit.   This  is  useful,  for
              example,  in  identifying  regions  of  high  score  density  for  use in resolving
              overlapping hits from different models.

       --hmmout <f>
              If <queryfile> is sequence-based, the internally-computed  HMM(s)  are  written  to
              <f>.

       --acc  Use  accessions  instead  of names in the main output, where available for profiles
              and/or sequences.

       --noali
              Omit the alignment section from the main output. This can greatly reduce the output
              volume.

       --notextw
              Unlimit  the  length of each line in the main output. The default is a limit of 120
              characters per line, which helps in displaying the output cleanly on terminals  and
              in editors, but can truncate target profile description lines.

       --textw <n>
              Set  the main output's line length limit to <n> characters per line. The default is
              120.

OPTIONS CONTROLLING REPORTING THRESHOLDS

       Reporting thresholds control which hits are reported in output  files  (the  main  output,
       --tblout, and --dfamtblout).  Hits are ranked by statistical significance (E-value).

       -E <x> Report  target  sequences  with an E-value of <= <x>.  The default is 10.0, meaning
              that on average, about 10 false positives will be reported per query,  so  you  can
              see the top of the noise and decide for yourself if it's really noise.

       -T <x> Instead  of  thresholding output on E-value, instead report target sequences with a
              bit score of >= <x>.

OPTIONS FOR INCLUSION THRESHOLDS

       Inclusion thresholds are stricter than reporting thresholds.  Inclusion thresholds control
       which hits are considered to be reliable enough to be included in an output alignment or a
       subsequent search round, or marked as significant ("!") as opposed to  questionable  ("?")
       in hit output.

       --incE <x>
              Use  an E-value of <= <x> as the inclusion threshold.  The default is 0.01, meaning
              that on average, about 1 false positive would be expected  in  every  100  searches
              with different query sequences.

       --incT <x>
              Instead  of  using E-values for setting the inclusion threshold, use a bit score of
              >= <x> as the inclusion threshold.  By default this option is unset.

OPTIONS FOR MODEL-SPECIFIC SCORE THRESHOLDING

       Curated profile databases may define specific  bit  score  thresholds  for  each  profile,
       superseding any thresholding based on statistical significance alone.

       To  use  these  options,  the  profile  must  contain  the appropriate (GA, TC, and/or NC)
       optional score threshold annotation; this is picked up by hmmbuild from  Stockholm  format
       alignment  files.  For  a  nucleotide model, each thresholding option has a single per-hit
       threshold <x> This acts as if -T<x> --incT<x> has been  applied  specifically  using  each
       model's curated thresholds.

       --cut_ga
              Use  the  GA  (gathering) bit score threshold in the model to set per-hit reporting
              and inclusion thresholds. GA thresholds are generally considered to be the reliable
              curated  thresholds  defining  family  membership;  for  example,  in  Dfam,  these
              thresholds are applied when annotating a genome with a model of a family  known  to
              be  found  in  that  organism.  They may allow for minimal expected false discovery
              rate.

       --cut_nc
              Use the NC (noise cutoff) bit score threshold in the model to set per-hit reporting
              and  inclusion thresholds. NC thresholds are less stringent than GA; in the context
              of Pfam, they are generally used to store the score of  the  highest-scoring  known
              false positive.

       --cut_tc
              Use  the  NC  (trusted  cutoff)  bit  score  threshold  in the model to set per-hit
              reporting and inclusion thresholds. TC thresholds are more stringent than  GA,  and
              are  generally considered to be the score of the lowest-scoring known true positive
              that is above all known false positives; for example, in Dfam, these thresholds are
              applied  when annotating a genome with a model of a family not known to be found in
              that organism.

OPTIONS CONTROLLING THE ACCELERATION PIPELINE

HMMER3 searches are accelerated in a three-step filter pipeline: the scanning-SSV filter,
the Viterbi filter, and the Forward filter. The first filter is the fastest and most
approximate; the last is the full Forward scoring algorithm. There is also a bias filter
step between SSV and Viterbi. Targets that pass all the steps in the acceleration pipeline
are then subjected to postprocessing -- domain identification and scoring using the
Forward/Backward algorithm.

Changing filter thresholds only removes or includes targets from consideration; changing
filter thresholds does not alter bit scores, E-values, or alignments, all of which are
determined solely in postprocessing.

--max Turn off (nearly) all filters, including the bias filter, and run full
Forward/Backward postprocessing on most of the target sequence. In contrast to
hmmscan, the --max flag in nhmmscan sets the scanning-SSV filter threshold to 0.4,
not 1.0. Use of this flag increases sensitivity somewhat, at a large cost in speed.

--F1 <x>
Set the P-value threshold for the SSV filter step. The default is 0.02, meaning
that roughly 2% of the highest scoring nonhomologous targets are expected to pass
the filter.

--F2 <x>
Set the P-value threshold for the Viterbi filter step. The default is 0.001.

--F3 <x>
Set the P-value threshold for the Forward filter step. The default is 1e-5.

--nobias
Turn off the bias filter. This increases sensitivity somewhat, but can come at a
high cost in speed, especially if the query has biased residue composition (such as
a repetitive sequence region, or if it is a membrane protein with large regions of
hydrophobicity). Without the bias filter, too many sequences may pass the filter
with biased queries, leading to slower than expected performance as the
computationally intensive Forward/Backward algorithms shoulder an abnormally heavy
load.

OTHER OPTIONS

--tformat <s>
Assert that the target sequence database file is in format <s>. Accepted formats
include fasta, embl, genbank, ddbj, uniprot, stockholm, pfam, a2m, and afa. The
default is to autodetect the format of the file.

--qformat <s>
Declare that the input queryfile is in format <s>. This is used when the query is
sequence-based, rather than made up of profile model(s). Currently the accepted
multiple alignment sequence file formats include Stockholm, Aligned FASTA, Clustal,
NCBI PSI-BLAST, PHYLIP, Selex, and UCSC SAM A2M. Default is to autodetect the
format of the file.

--nonull2
Turn off the null2 score corrections for biased composition.

-Z <x> For the purposes of per-hit E-value calculations, Assert that the total size of the
target database is <x> million nucleotides, rather than the actual number of
targets seen.

--seed <n>
Set the random number seed to <n>. Some steps in postprocessing require Monte
Carlo simulation. The default is to use a fixed seed (42), so that results are
exactly reproducible. Any other positive integer will give different (but also
reproducible) results. A choice of 0 uses a randomly chosen seed.

--w_beta <x>
Window length tail mass. The upper bound, W, on the length at which nhmmer expects
to find an instance of the model is set such that the fraction of all sequences
generated by the model with length >= W is less than <x>. The default is 1e-7.
This flag may be used to override the value of W established for the model by
hmmbuild, or when the query is sequence-based.

--w_length <n>
Override the model instance length upper bound, W, which is otherwise controlled by
--w_beta. It should be larger than the model length. The value of W is used deep
in the acceleration pipeline, and modest changes are not expected to impact results
(though larger values of W do lead to longer run time). This flag may be used to
override the value of W established for the model by hmmbuild, or when the query is
sequence-based.

--toponly
Only search the top strand. By default both the query sequence and its reverse-
complement are searched.

--bottomonly
Only search the bottom (reverse-complement) strand. By default both the query
sequence and its reverse-complement are searched.

--cpu <n>
Set the number of parallel worker threads to <n>. By default, HMMER sets this to
the number of CPU cores it detects in your machine - that is, it tries to maximize
the use of your available processor cores. Setting <n> higher than the number of
available cores is of little if any value, but you may want to set it to something
less. You can also control this number by setting an environment variable,
HMMER_NCPU.

This option is only available if HMMER was compiled with POSIX threads support.
This is the default, but it may have been turned off at compile-time for your site
or machine for some reason.

--stall
For debugging the MPI master/worker version: pause after start, to enable the
developer to attach debuggers to the running master and worker(s) processes. Send
SIGCONT signal to release the pause. (Under gdb: (gdb) signal SIGCONT) (Only
available if optional MPI support was enabled at compile-time.)

--mpi Run in MPI master/worker mode, using mpirun. (Only available if optional MPI
support was enabled at compile-time.)

COPYRIGHT

       Copyright (C) 2013 Howard Hughes Medical Institute.
       Freely distributed under the GNU General Public License (GPLv3).

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

AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org