nhmmscan - Online in the Cloud

PROGRAM:

NAME

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

SYNOPSIS

hmmscan [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 hmmscan.
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 those 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 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.

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 the query sequence 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.

--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.

--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 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.)

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