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PROGRAM:

NAME


cmscan - search sequence(s) against a covariance model database

SYNOPSIS


cmscan [options] <cmdb> <seqfile>

DESCRIPTION


cmscan is used to search sequences against collections of covariance models. For each
sequence in <seqfile>, use that query sequence to search the target database of CMs in
<cmdb>, and output ranked lists of the CMs 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 among others), or in
alignment file formats (stockholm, aligned fasta, and others). See the --qformat option
for a complete list.

The <cmdb> needs to be press'ed using cmpress before it can be searched with cmscan. This
creates four binary files, suffixed .i1{fimp}. Additionally, <cmdb> must have been
calibrated for E-values with cmcalibrate before being press'ed with cmpress.

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 <cmdb> cannot be read from a <stdin>
stream, because it needs to have those four auxiliary binary files generated by cmpress.

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.

cmscan reexamines the 5' and 3' termini of target sequences using specialized algorithms
for detection of truncated hits, in which part of the 5' and/or 3' end of the actual full
length homologous sequence is missing in the target sequence file. These types of hits
will be most common in sequence files consisting of unassembled sequencing reads. By
default, any 5' truncated hit is required to include the first residue of the target
sequence it derives from in <seqfile>, and any 3' truncated hit is required to include the
final residue of the target sequence it derives from. Any 5' and 3' truncated hit must
include the first and final residue of the target sequence it derives from. The --anytrunc
option will relax the requirements for hit inclusion of sequence endpoints, and truncated
hits are allowed to start and stop at any positions of target sequences. Importantly
though, with --anytrunc, hit E-values will be less accurate because model calibration does
not consider the possibility of truncated hits, so use it with caution. The --notrunc
option can be used to turn off truncated hit detection. --notrunc will reduce the running
time of cmscan, most significantly for target <seqfile> files that include many short
sequences. Truncated hit detection is automatically turned off when the --max, --nohmm,
--qdb, or --nonbanded options are used because it relies on the use of an accelerated HMM
banded alignment strategy that is turned off by any of those options.

OPTIONS


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

-g Turn on the glocal alignment algorithm, global with respect to the query model and
local with respect to the target database. By default, the local alignment
algorithm is used which is local with respect to both the target sequence and the
model. In local mode, the alignment to span two or more subsequences if necessary
(e.g. if the structures of the query model and target sequence are only partially
shared), allowing certain large insertions and deletions in the structure to be
penalized differently than normal indels. Local mode performs better on empirical
benchmarks and is significantly more sensitive for remote homology detection.
Empirically, glocal searches return many fewer hits than local searches, so glocal
may be desired for some applications.

-Z <x> Calculate E-values as if the search space size was <x> megabases (Mb). Without the
use of this option, the search space size changes for each query sequence, it is
defined as the length of the current query sequence times 2 (because both strands
of the sequence will be searched) times the number of CMs in <cmdb>.

--devhelp
Print help, as with -h , but also include expert options that are not displayed
with -h . These expert options are not expected to be relevant for the vast
majority of users and so are not described in the manual page. The only resources
for understanding what they actually do are the brief one-line descriptions output
when --devhelp is enabled, and the source code.

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 hits found, with one
data line per hit. The format of this file is described in the Infernal user
guide.

--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.

--verbose
Include extra search pipeline statistics in the main output, including filter
survival statistics for truncated hit detection and number of envelopes discarded
due to matrix size overflows.

OPTIONS CONTROLLING REPORTING THRESHOLDS


Reporting thresholds control which hits are reported in output files (the main output and
--tblout) Hits are ranked by statistical significance (E-value). By default, all hits
with an E-value <= 10 are reported. The following options allow you to change the default
E-value reporting thresholds, or to use bit score thresholds instead.

-E <x> In the per-target output, 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 per-CM output on E-value, 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 a possible subsequent
search round, or marked as significant ("!") as opposed to questionable ("?") in hit
output.

--incE <x>
Use an E-value of <= <x> as the hit 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 hit inclusion threshold. By default this option is unset.

OPTIONS FOR MODEL-SPECIFIC SCORE THRESHOLDING


Curated CM databases may define specific bit score thresholds for each CM, 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 cmbuild from Stockholm format
alignment files. Each thresholding option has a score of <x> bits, and acts as if -T <x>
--incT <x> has been applied specifically using each model's curated thresholds.

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

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

--cut_tc
Use the TC (trusted cutoff) bit score thresholds in the model to set hit 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.

OPTIONS CONTROLLING THE ACCELERATION PIPELINE


Infernal 1.1 searches are accelerated in a six-stage filter pipeline. The first five
stages use a profile HMM to define envelopes that are passed to the stage six CM CYK
filter. Any envelopes that survive all filters are assigned final scores using the the CM
Inside algorithm.

The profile HMM filter is built by the cmbuild program and is stored in <cmfile>.

Each successive filter is slower than the previous one, but better than it at
disciminating between subsequences that may contain high-scoring CM hits and those that do
not. The first three HMM filter stages are the same as those used in HMMER3. Stage 1 (F1)
is the local HMM SSV filter modified for long sequences. Stage 2 (F2) is the local HMM
Viterbi filter. Stage 3 (F3) is the local HMM Forward filter. Each of the first three
stages uses the profile HMM in local mode, which allows a target subsequence to align to
any region of the HMM. Stage 4 (F4) is a glocal HMM filter, which requires a target
subsequence to align to the full-length profile HMM. Stage 5 (F5) is the glocal HMM
envelope definition filter, which uses HMMER3's domain identification heursitics to define
envelope boundaries. After each stage from 2 to 5 a bias filter step (F2b, F3b, F4b, and
F5b) is used to remove sequences that appear to have passed the filter due to biased
composition alone. Any envelopes that survive stages F1 through F5b are then passed with
the local CM CYK filter. The CYK filter uses constraints (bands) derived from an HMM
alignment of the envelope to reduce the number of required calculations and save time.
Any envelopes that pass CYK are scored with the local CM Inside algorithm, again using HMM
bands for acceleration.

The default filter thresholds that define the minimum score required for a subsequence to
survive each stage are defined based on the size of the search space (Z), which is defined
as the length of the current query sequence times 2 (because both strands will be
searched) times the number of profiles in <cmdb>. However, if either the -Z <x> or --FZ
<x> options are used then the search space will be considered to be <x> for purposes of
defining the filter thresholds.

For larger databases, the filters are more strict leading to more acceleration but
potentially a greater loss of sensitivity. The rationale is that for larger databases,
hits must have higher scores to achieve statistical significance, so stricter filtering
that removes lower scoring insignificant hits is acceptable.

The P-value thresholds for all possible search space sizes and all filter stages are
listed next. (A P-value threshold of 0.01 means that roughly 1% of the highest scoring
nonhomologous subsequence are expected to pass the filter.) Z is defined as the number of
nucleotides in the complete target sequence file times 2 because both strands will be
searched with each model.

If Z is less than 2 Mb: F1 is 0.35; F2 and F2b are off; F3, F3b, F4, F4b and F5 are 0.02;
F6 is 0.0001.

If Z is between 2 Mb and 20 Mb: F1 is 0.35; F2 and F2b are off; F3, F3b, F4, F4b and F5
are 0.005; F6 is 0.0001.

If Z is between 20 Mb and 200 Mb: F1 is 0.35; F2 and F2b are 0.15; F3, F3b, F4, F4b and F5
are 0.003; F6 is 0.0001.

If Z is between 200 Mb and 2 Gb: F1 is 0.15; F2 and F2b are 0.15; F3, F3b, F4, F4b, F5,
and F5b are 0.0008; and F6 is 0.0001.

If Z is between 2 Gb and 20 Gb: F1 is 0.15; F2 and F2b are 0.15; F3, F3b, F4, F4b, F5, and
F5b are 0.0002; and F6 is 0.0001.

If Z is more than 20 Gb: F1 is 0.06; F2 and F2b are 0.02; F3, F3b, F4, F4b, F5, and F5b
are 0.0002; and F6 is 0.0001.

These thresholds were chosen based on performance on an internal benchmark testing many
different possible settings.

There are five options for controlling the general filtering level. These options are, in
order from least strict (slowest but most sensitive) to most strict (fastest but least
sensitive): --max, --nohmm, --mid, --default, (this is the default setting) --rfam. and
--hmmonly. With --default the filter thresholds will be database-size dependent. See the
explanation of each of these individual options below for more information.

Additionally, an expert user can precisely control each filter stage score threshold with
the --F1, --F1b, --F2, --F2b, --F3, --F3b, --F4, --F4b, --F5, --F5b, and --F6 options. As
well as turn each stage on or off with the --noF1, --doF1b, --noF2, --noF2b, --noF3,
--noF3b, --noF4, --noF4b, --noF5, and --noF6. options. These options are only displayed
if the --devhelp option is used to keep the number of displayed options with -h
reasonable, and because they are only expected to be useful to a small minority of users.

As a special case, for any models in <cmfile> which have zero basepairs, profile HMM
searches are run instead of CM searches. HMM algorithms are more efficient than CM
algorithms, and the benefit of CM algorithms is lost for models with no secondary
structure (zero basepairs). These profile HMM searches will run significantly faster than
the CM searches. You can force HMM-only searches with the --hmmonly option. For more
information on HMM-only searches see the user guide.

--max Turn off all filters, and run non-banded Inside on every full-length target
sequence. This increases sensitivity somewhat, at an extremely large cost in speed.

--nohmm
Turn off all HMM filter stages (F1 through F5b). The CYK filter, using QDBs, will
be run on every full-length target sequence and will enforce a P-value threshold of
0.0001. Each subsequence that survives CYK will be passed to Inside, which will
also use QDBs (but a looser set). This increases sensitivity somewhat, at a very
large cost in speed.

--mid Turn off the HMM SSV and Viterbi filter stages (F1 through F2b). Set remaining HMM
filter thresholds (F3 through F5b) to 0.02 by default, but changeable to <x> with
--Fmid <x> sequence. This may increase sensitivity, at a significant cost in speed.

--default
Use the default filtering strategy. This option is on by default. The filter
thresholds are determined based on the database size.

--rfam Use a strict filtering strategy devised for large databases (more than 20 Gb). This
will accelerate the search at a potential cost to sensitivity.

--hmmonly
Only use the filter profile HMM for searches, do not use the CM. Only filter
stages F1 through F3 will be executed, using strict P-value thresholds (0.02 for
F1, 0.001 for F2 and 0.00001 for F3). Additionally a bias composition filter is
used after the F1 stage (with P=0.02 survival threshold). Any hit that survives
all stages and has an HMM E-value or bit score above the reporting threshold will
be output. The user can change the HMM-only filter thresholds and options with
--hmmF1, --hmmF2, --hmmF3, --hmmnobias, --hmmnonull2, and --hmmmax. By default,
searches for any model with zero basepairs will be run in HMM-only mode. This can
be turned off, forcing CM searches for these models with the --nohmmonly option.

--FZ <x>
Set filter thresholds as the defaults used if the database were <x> megabases (Mb).
If used with <x> greater than 20000 (20 Gb) this option has the same effect as
--rfam.

--Fmid <x>
With the --mid option set the HMM filter thresholds (F3 through F5b) to <x>. By
default, <x> is 0.02.

OTHER OPTIONS


--notrunc
Turn off truncated hit detection.

--anytrunc
Allow truncated hits to begin and end at any position in a target sequence. By
default, 5' truncated hits must include the first residue of their target sequence
and 3' truncated hits must include the final residue of their target sequence. With
this option you may observe fewer full length hits that extend to the beginning and
end of the query CM.

--nonull3
Turn off the null3 CM score corrections for biased composition. This correction is
not used during the HMM filter stages.

--mxsize <x>
Set the maximum allowable CM DP matrix size to <x> megabytes. By default this size
is 128 Mb. This should be large enough for the vast majority of searches,
especially with smaller models. If cmsearch encounters an envelope in the CYK or
Inside stage that requires a larger matrix, the envelope will be discounted from
consideration. This behavior is like an additional filter that prevents expensive
(slow) CM DP calculations, but at a potential cost to sensitivity. Note that if
cmsearch is being run in <n> multiple threads on a multicore machine then each
thread may have an allocated matrix of up to size <x> Mb at any given time.

--smxsize <x>
Set the maximum allowable CM search DP matrix size to <x> megabytes. By default
this size is 128 Mb. This option is only relevant if the CM will not use HMM
banded matrices, i.e. if the --max, --nohmm, --qdb, --fqdb, --nonbanded, or
--fnonbanded options are also used. Note that if cmsearch is being run in <n>
multiple threads on a multicore machine then each thread may have an allocated
matrix of up to size <x> Mb at any given time.

--cyk Use the CYK algorithm, not Inside, to determine the final score of all hits.

--acyk Use the CYK algorithm to align hits. By default, the Durbin/Holmes optimal accuracy
algorithm is used, which finds the alignment that maximizes the expected accuracy
of all aligned residues.

--wcx <x>
For each CM, set the W parameter, the expected maximum length of a hit, to <x>
times the consensus length of the model. By default, the W parameter is read from
the CM file and was calculated based on the transition probabilities of the model
by cmbuild. You can find out what the default W is for a model using cmstat. This
option should be used with caution as it impacts the filtering pipeline at several
different stages in nonobvious ways. It is only recommended for expert users
searching for hits that are much longer than any of the homologs used to build the
model in cmbuild, e.g. ones with large introns or other large insertions. It
cannot be used in combination with the --nohmm, --fqdb or --qdb options because in
those cases W is limited by query-dependent bands.

--toponly
Only search the top (Watson) strand of target sequences in <seqfile>. By default,
both strands are searched. This will halve the search space size (Z).

--bottomonly
Only search the bottom (Crick) strand of target sequences in <seqfile>. By
default, both strands are searched. This will halve the search space size (Z).

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

--glist <f>
Configure a subset of models from <cmfile> in glocal alignment mode, instead of
local mode, namely the models listed in file <f>. Configure all other models
(those not listed in <f>) in local mode. This option is incompatible with -g.
File <f> must list valid names of models from <cmfile>, each separated by any
whitespace character (e.g. a newline character).

--cpu <n>
Set the number of parallel worker threads to <n>. By default, Infernal 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, INFERNAL_NCPU. This option is only available if Infernal 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.)

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