Ubuntu Manpage: nhmmscan - search DNA sequence(s) against a DNA profile database

NAME

       nhmmscan - search DNA sequence(s) against a DNA profile database

SYNOPSIS

       nhmmscan [options] hmmdb seqfile

DESCRIPTION

       nhmmscan  is  used  to  search  nucleotide  sequences  against  collections  of nucleotide
       profiles. For each sequence in seqfile, use that  query  sequence  to  search  the  target
       database  of  profiles  in  hmmdb,  and  output ranked lists of the profiles with the most
       significant matches to the sequence.

       The seqfile may contain more than one query sequence.  It  can  be  in  FASTA  format,  or
       several  other common sequence file formats (genbank, embl, and uniprot, among others), or
       in alignment file formats (stockholm, aligned fasta, and others). See the --qformat option
       for a complete list.

       The  hmmdb  needs  to  be press'ed using hmmpress before it can be searched with nhmmscan.
       This creates four binary files, suffixed .h3{fimp}.

       The query seqfile may be '-' (a dash character), in which case  the  query  sequences  are
       read  from  a  stdin  pipe  instead of from a file.  The hmmdb cannot be read from a stdin
       stream, because it needs to have the four auxiliary binary files generated by hmmpress.

       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.

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

       --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 FOR 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  profiles  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 profiles 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.  In nhmmscan, which does not  have  any  alignment  output  (like
       nhmmer), inclusion thresholds have little effect. They only affect what hits get marked as
       significant (!) or 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.  It would be unusual to use bit score thresholds
              with hmmscan, because you don't  expect  a  single  score  threshold  to  work  for
              different  profiles;  different  profiles  have  slightly  different expected score
              distributions.

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  TC  (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.

CONTROL OF 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, where this flag really does turn off the filters entirely, 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 MSV 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

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

-Z <x> Assert that the total number of targets in your searches is <x>, for the purposes
of per-sequence E-value calculations, 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 an arbitrarily chosen seed.

--qformat <s>
Assert that input query seqfile is in format <s>, bypassing format autodetection.
Common choices for <s> include: fasta, embl, genbank. Alignment formats also work;
common choices include: stockholm, a2m, afa, psiblast, clustal, phylip. For more
information, and for codes for some less common formats, see main documentation.
The string <s> is case-insensitive (fasta or FASTA both work).

--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.

--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.

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

--crick
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>. The default is 0, meaning off
(no thread-level parallelization), because nhmmscan is typically i/o bound and the
extra overhead of our current multithreaded implementation isn't worthwhile. You
can also control this number by setting an environment variable, HMMER_NCPU. There
is also a master thread, so the actual number of threads that HMMER spawns is at
least <n>+1.

This option is not available if HMMER was compiled with POSIX threads support
turned off.

--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 under MPI control with master/worker parallelization (using mpirun, for
example, or equivalent). Only available if optional MPI support was enabled at
compile-time.

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