Ubuntu Manpage: hmmscan - search protein sequence(s) against a protein profile database

NAME

       hmmscan - search protein sequence(s) against a protein profile database

SYNOPSIS

       hmmscan [options] <hmmdb> <seqfile>

DESCRIPTION

       hmmscan  is  used to search protein sequences against collections of protein 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 and --domtblout  options
       save output in simple tabular formats that are 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-target  output,
              with one data line per homologous target model found.

       --domtblout <f>
              Save  a  simple  tabular  (space-delimited) file summarizing the per-domain output,
              with one data line per homologous domain detected in  a  query  sequence  for  each
              homologous model.

       --pfamtblout <f>
              Save  an  especially  succinct  tabular (space-delimited) file summarizing the per-
              target output, with one data line per homologous target model found.

       --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 --domtblout).

       -E <x> In the per-target output, 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  per-profile  output  on  E-value,  instead report target
              profiles with a bit score of >= <x>.

       --domE <x>
              In the per-domain output, for target profiles that have already satisfied the  per-
              profile  reporting  threshold, report individual domains with a conditional E-value
              of <= <x>.  The default is 10.0.  A conditional E-value means the  expected  number
              of  additional  false  positive  domains  in  the  smaller  search  space  of those
              comparisons that already satisfied the per-profile reporting  threshold  (and  thus
              must have at least one homologous domain already).

       --domT <x>
              Instead of thresholding per-domain output on E-value, instead report domains 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 hmmscan, which does  not  have  any  alignment  output  (like
       hmmsearch or phmmer) nor any iterative search steps (like jackhmmer), inclusion thresholds
       have little effect. They only affect  what  domains  get  marked  as  significant  (!)  or
       questionable (?) in domain output.

       --incE <x>
              Use  an  E-value  of  <= <x> as the per-target 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, instead use a bit
              score of >= <x> as the per-target 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.

       --incdomE <x>
              Use  a  conditional  E-value  of  <=  <x> as the per-domain inclusion threshold, in
              targets that have already satisfied the  overall  per-target  inclusion  threshold.
              The default is 0.01.

       --incdomT <x>
              Instead  of  using  E-values,  instead  use a bit score of >= <x> as the per-domain
              inclusion threshold.  As with --incT above, it would be unusual to use a single bit
              score threshold in hmmscan.

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. Each thresholding option has two scores: the per-sequence threshold  <x1>
       and   the  per-domain  threshold  <x2>  These  act  as  if  -T<x1>  --incT<x1>  --domT<x2>
       --incdomT<x2> has been applied specifically using each model's curated thresholds.

       --cut_ga
              Use the GA (gathering) bit scores in the model to set per-sequence (GA1)  and  per-
              domain  (GA2)  reporting  and  inclusion  thresholds.  GA  thresholds are generally
              considered to be the reliable curated thresholds defining  family  membership;  for
              example,  in  Pfam,  these  thresholds  define  what  gets  included  in  Pfam Full
              alignments based on searches with Pfam Seed models.

       --cut_nc
              Use the NC (noise cutoff) bit score thresholds in the  model  to  set  per-sequence
              (NC1)  and  per-domain  (NC2) reporting and inclusion thresholds. NC thresholds are
              generally considered to be the score of the highest-scoring known false positive.

       --cut_tc
              Use the NC (trusted cutoff) bit score thresholds in the model to  set  per-sequence
              (TC1)  and  per-domain  (TC2) reporting and inclusion thresholds. TC thresholds are
              generally considered to be the score of the lowest-scoring known true positive that
              is above all known false positives.

CONTROL OF THE ACCELERATION PIPELINE

HMMER3 searches are accelerated in a three-step filter pipeline: the MSV 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 MSV 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 all filters, including the bias filter, and run full Forward/Backward
postprocessing on every target. This 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.

--domZ <x>
Assert that the total number of targets in your searches is <x>, for the purposes
of per-domain conditional E-value calculations, rather than the number of targets
that passed the reporting thresholds.

--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.

--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.