NAME¶
hmmbuild - construct profile HMM(s) from multiple sequence alignment(s)
SYNOPSIS¶
hmmbuild [options] hmmfile msafile
DESCRIPTION¶
Build a profile HMM for each multiple sequence alignment in
msafile, and
save it to a new file
hmmfile.
OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and all
available options.
- -n <s>
- Name the new profile <s>. The default is to
use the name of the alignment (if one is present in the msafile,
or, failing that, the name of the hmmfile. If msafile
contains more than one alignment, -n doesn't work, and every
alignment must have a name annotated in the msafile (as in
Stockholm #=GF ID annotation).
- -o <f>
- Direct the summary output to file <f>, rather
than to stdout.
- -O <f>
- After each model is constructed, resave annotated, possibly
modified source alignments to a file <f> in Stockholm format.
The alignments are annotated with a reference annotation line indicating
which columns were assigned as consensus, and sequences are annotated with
what relative sequence weights were assigned. Some residues of the
alignment may have been shifted to accommodate restrictions of the Plan7
profile architecture, which disallows transitions between insert and
delete states.
OPTIONS FOR SPECIFYING THE ALPHABET¶
The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking at
the composition of the
msafile. Autodetection is normally quite
reliable, but occasionally alphabet type may be ambiguous and autodetection
can fail (for instance, on tiny toy alignments of just a few residues). To
avoid this, or to increase robustness in automated analysis pipelines, you may
specify the alphabet type of
msafile with these options.
- --amino
- Specify that all sequences in msafile are proteins.
- --dna
- Specify that all sequences in msafile are DNAs.
- --rna
- Specify that all sequences in msafile are RNAs.
OPTIONS CONTROLLING PROFILE CONSTRUCTION¶
These options control how consensus columns are defined in an alignment.
- --fast
- Define consensus columns as those that have a fraction
>= symfrac of residues as opposed to gaps. (See below for the
--symfrac option.) This is the default.
- --hand
- Define consensus columns in next profile using reference
annotation to the multiple alignment. This allows you to define any
consensus columns you like.
- --symfrac <x>
- Define the residue fraction threshold necessary to define a
consensus column when using the default --fast construction option.
The default for --symfrac is 0.5. The symbol fraction in each
column is calculated after taking relative sequence weighting into
account, and ignoring gap characters corresponding to ends of sequence
fragments (as opposed to internal insertions/deletions). Setting this to
0.0 means that every alignment column will be assigned as consensus, which
may be useful in some cases. Setting it to 1.0 means that only columns
that have no gap characters at all will be assigned as consensus.
- --fragthresh <x>
- We only want to count terminal gaps as deletions if the
aligned sequence is known to be full-length, not if it is a fragment (for
instance, because only part of it was sequenced). HMMER uses a simple rule
to infer fragments: if the sequence length L is less than a fraction
<x> times the mean sequence length of all the sequences in
the alignment, then the sequence is handled as a fragment. The default is
0.5.
OPTIONS CONTROLLING RELATIVE WEIGHTS¶
HMMER uses an ad hoc sequence weighting algorithm to downweight closely related
sequences and upweight distantly related ones. This has the effect of making
models less biased by uneven phylogenetic representation. For example, two
identical sequences would typically each receive half the weight that one
sequence would. These options control which algorithm gets used.
- --wpb
- Use the Henikoff position-based sequence weighting scheme
[Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
- --wgsc
- Use the Gerstein/Sonnhammer/Chothia weighting algorithm
[Gerstein et al, J. Mol. Biol. 235:1067, 1994].
- --wblosum
- Use the same clustering scheme that was used to weight data
in calculating BLOSUM subsitution matrices [Henikoff and Henikoff, Proc.
Natl. Acad. Sci 89:10915, 1992]. Sequences are single-linkage clustered at
an identity threshold (default 0.62; see --wid) and within each
cluster of c sequences, each sequence gets relative weight 1/c.
- --wnone
- No relative weights. All sequences are assigned uniform
weight.
- --wid <x>
- Sets the identity threshold used by single-linkage
clustering when using --wblosum. Invalid with any other weighting
scheme. Default is 0.62.
OPTIONS CONTROLLING EFFECTIVE SEQUENCE NUMBER¶
After relative weights are determined, they are normalized to sum to a total
effective sequence number,
eff_nseq. This number may be the actual
number of sequences in the alignment, but it is almost always smaller than
that. The default entropy weighting method
(--eent) reduces the
effective sequence number to reduce the information content (relative entropy,
or average expected score on true homologs) per consensus position. The target
relative entropy is controlled by a two-parameter function, where the two
parameters are settable with
--ere and
--esigma.
- --eent
- Adjust effective sequence number to achieve a specific
relative entropy per position (see --ere). This is the default.
- --eclust
- Set effective sequence number to the number of
single-linkage clusters at a specific identity threshold (see
--eid). This option is not recommended; it's for experiments
evaluating how much better --eent is.
- --enone
- Turn off effective sequence number determination and just
use the actual number of sequences. One reason you might want to do this
is to try to maximize the relative entropy/position of your model, which
may be useful for short models.
- --eset <x>
- Explicitly set the effective sequence number for all models
to <x>.
- --ere <x>
- Set the minimum relative entropy/position target to
<x>. Requires --eent. Default depends on the sequence
alphabet; for protein sequences, it is 0.59 bits/position.
- --esigma <x>
- Sets the minimum relative entropy contributed by an entire
model alignment, over its whole length. This has the effect of making
short models have higher relative entropy per position than --ere
alone would give. The default is 45.0 bits.
- --eid <x>
- Sets the fractional pairwise identity cutoff used by single
linkage clustering with the --eclust option. The default is 0.62.
OPTIONS CONTROLLING E-VALUE CALIBRATION¶
The location parameters for the expected score distributions for MSV filter
scores, Viterbi filter scores, and Forward scores require three short random
sequence simulations.
- --EmL <n>
- Sets the sequence length in simulation that estimates the
location parameter mu for MSV filter E-values. Default is 200.
- --EmN <n>
- Sets the number of sequences in simulation that estimates
the location parameter mu for MSV filter E-values. Default is 200.
- --EvL <n>
- Sets the sequence length in simulation that estimates the
location parameter mu for Viterbi filter E-values. Default is 200.
- --EvN <n>
- Sets the number of sequences in simulation that estimates
the location parameter mu for Viterbi filter E-values. Default is 200.
- --EfL <n>
- Sets the sequence length in simulation that estimates the
location parameter tau for Forward E-values. Default is 100.
- --EfN <n>
- Sets the number of sequences in simulation that estimates
the location parameter tau for Forward E-values. Default is 200.
- --Eft <x>
- Sets the tail mass fraction to fit in the simulation that
estimates the location parameter tau for Forward evalues. Default is 0.04.
OTHER OPTIONS¶
- --mpi
- Run as a parallel MPI program. Each alignment is assigned
to a MPI worker node for construction. (Therefore, the maximum
parallelization cannot exceed the number of alignments in the input
msafile.) This is useful when building large profile libraries.
This option is only available if optional MPI capability was enabled at
compile-time.
- --informat <s>
- Declare that the input msafile is in format
<s>. Currently the accepted multiple alignment sequence file
formats only include Stockholm and SELEX. Default is to autodetect the
format of the file.
- --seed <n>
- Seed the random number generator with <n>, an
integer >= 0. If <n> is nonzero, any stochastic
simulations will be reproducible; the same command will give the same
results. If <n> is 0, the random number generator is seeded
arbitrarily, and stochastic simulations will vary from run to run of the
same command. The default seed is 42.
--laplace Experimental only: use a Laplace +1 prior in place of the
default mixture Dirichlet prior.
- --stall
- For debugging MPI parallelization: arrest program execution
immediately after start, and wait for a debugger to attach to the running
process and release the arrest.
SEE ALSO¶
See
hmmer(1) for a master man page with a list of all the individual man
pages for programs in the HMMER package.
For complete documentation, see the user guide that came with your HMMER
distribution (Userguide.pdf); or see the HMMER web page (@HMMER_URL@).
COPYRIGHT¶
@HMMER_COPYRIGHT@
@HMMER_LICENSE@
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page
(@HMMER_URL@).
AUTHOR¶
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org