hmmbuild(1) HMMER Manual hmmbuild(1)NAMEhmmbuild - construct profile HMM(s) from multiple sequence alignment(s)SYNOPSIShmmbuild [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 mod‐
ified source alignments to a file <f> in Stockholm format. The
alignments are annotated with a reference annotation line indi‐
cating 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 accommo‐
date restrictions of the Plan7 profile architecture, which dis‐
allows 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 align‐
ment.
--fast Define consensus columns as those that have a fraction >= sym‐
frac of residues as opposed to gaps. (See below for the --sym‐
frac option.) This is the default.
--hand Define consensus columns in next profile using reference annota‐
tion 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 con‐
sensus 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/dele‐
tions). 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 representa‐
tion. 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 [Ger‐
stein 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 con‐
sensus 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 loca‐
tion 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 loca‐
tion 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 loca‐
tion 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 esti‐
mates 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 paral‐
lelization 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
HMMER @HMMER_VERSION@ @HMMER_DATE@ hmmbuild(1)
