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[options] hmmfile alignfile
hmmbuild reads a multiple
sequence alignment file alignfile , builds a new profile HMM, and saves
the HMM in hmmfile.
alignfile may be in ClustalW, GCG MSF, or SELEX alignment
By default, the model is configured to find one or more nonoverlapping
alignments to the complete model. This is analogous to the behavior of
the hmmls program of HMMER 1. To configure the model for a single global
alignment, use the -g option; to configure the model for multiple local
alignments a la the old program hmmfs, use the -f option; and to configure
the model for a single local alignment (a la standard Smith/Waterman,
or the old hmmsw program), use the -s option.
- [-f ] Configure the
model for finding multiple domains per sequence, where each domain can
be a local (fragmentary) alignment. This is analogous to the old hmmfs
program of HMMER 1.
- [-g ] Configure the model for finding a single global
alignment to a target sequence, analogous to the standard Needleman/Wunsch
algorithm or the old hmms program of HMMER 1.
- [-h ] Print brief help; includes
version number and summary of all options, including expert options.
<s> ] Name this HMM <s>. <s> can be any string of non-whitespace characters (e.g.
one "word"). There is no length limit (at least not one imposed by HMMER;
your shell will complain about command line lengths first).
- [-o <f> ] Re-save
the starting alignment to <f>, in SELEX format. The columns which were assigned
to match states will be marked with x's in an #=RF annotation line. If
either the -hand or -fast construction options were chosen, the alignment
may have been slightly altered to be compatible with Plan 7 transitions,
so saving the final alignment and comparing to the starting alignment
can let you view these alterations. See the User's Guide for more information
on this arcane side effect.
- [-s ] Configure the model for finding a single
local alignment per target sequence. This is analogous to the standard
Smith/Waterman algorithm or the hmmsw program of HMMER 1.
- [-A ] Append
this model to an existing hmmfile rather than creating hmmfile. Useful
for building HMM libraries (like Pfam).
- [-F ] Force overwriting of an existing
hmmfile. Otherwise HMMER will refuse to clobber your existing HMM files,
for safety's sake.
- [-amino ] Force the sequence alignment
to be interpreted as amino acid sequences. Normally HMMER autodetects whether
the alignment is protein or DNA, but sometimes alignments are so small
that autodetection is ambiguous. See -nucleic.
- [-archpri <x> ] Set the "architecture
prior" used by MAP architecture construction to <x>, where <x> is a probability
between 0 and 1. This parameter governs a geometric prior distribution
over model lengths. As <x> increases, longer models are favored a priori.
As <x> decreases, it takes more residue conservation in a column to make
a column a "consensus" match column in the model architecture. The 0.85
default has been chosen empirically as a reasonable setting.
- [-binary ] Write
the HMM to hmmfile in HMMER binary format instead of readable ASCII text.
- [-cfile <f> ] Save the observed emission and transition counts to <f> after
the architecture has been determined (e.g. after residues/gaps have been
assigned to match, delete, and insert states). This option is used in HMMER
development for generating data files useful for training new Dirichlet
priors. The format of count files is documented in the User's Guide.
] Quickly and heuristically determine the architecture of the model by
assigning all columns will more than a certain fraction of gap characters
to insert states. By default this fraction is 0.5, and it can be changed
using the -gapmax option. The default construction algorithm is a maximum
a posteriori (MAP) algorithm, which is slower.
- [-gapmax <x> ] Controls the
-fast model construction algorithm, but if -fast is not being used, has
no effect. If a column has more than a fraction <x> of gap symbols in it,
it gets assigned to an insert column. <x> is a frequency from 0 to 1, and
by default is set to 0.5. Higher values of <x> mean more columns get assigned
to consensus, and models get longer; smaller values of <x> mean fewer
columns get assigned to consensus, and models get smaller. <x>
- [-hand ] Specify
the architecture of the model by hand: the alignment file must be in SELEX
format, and the #=RF annotation line is used to specify the architecture.
Any column marked with a non-gap symbol (such as an 'x', for instance) is
assigned as a consensus (match) column in the model.
- [-idlevel <x> ] Controls
both the determination of effective sequence number and the behavior of
the -wblosum weighting option. The sequence alignment is clustered by
percent identity, and the number of clusters at a cutoff threshold of
<x> is used to determine the effective sequence number. Higher values of
<x> give more clusters and higher effective sequence numbers; lower values
of <x> give fewer clusters and lower effective sequence numbers. <x> is
a fraction from 0 to 1, and by default is set to 0.62 (corresponding to
the clustering level used in constructing the BLOSUM62 substitution matrix).
- [-noeff ] Turn off the effective sequence number calculation, and use the
true number of sequences instead. This will usually reduce the sensitivity
of the final model (so don't do it without good reason!)
- [-nucleic ] Force
the alignment to be interpreted as nucleic acid sequence, either RNA or
DNA. Normally HMMER autodetects whether the alignment is protein or DNA,
but sometimes alignments are so small that autodetection is ambiguous.
- [-null <f> ] Read a null model from <f>. The default for protein is
to use average amino acid frequencies from Swissprot 34 and p1 = 350/351;
for nucleic acid, the default is to use 0.25 for each base and p1 = 1000/1001.
For documentation of the format of the null model file and further explanation
of how the null model is used, see the User's Guide.
- [-pam <f> ] Apply a heuristic
PAM- (substitution matrix-) based prior instead of the default mixture Dirichlet.
The substitution matrix is read from <f>. See -pamwgt.
- [-pamwgt <x> ] Controls
the weight on a PAM-based prior. Only has effect if -pam option is also
in use. <x> is a positive real number, 20.0 by default. <x> is the number of
"pseudocounts" contriubuted by the heuristic prior. Very high values of
<x> can force a scoring system that is entirely driven by the substitution
matrix, making HMMER somewhat approximate Gribskov profiles.
- [-prior <f>
] Read a Dirichlet prior from <f>, replacing the default mixture Dirichlet.
The format of prior files is documented in the User's Guide, and an example
is given in the Demos directory of the HMMER distribution.
- [-swentry <x>
] Controls the total probability that is distributed to local entries into
the model, versus starting at the beginning of the model as in a global
alignment. <x> is a probability from 0 to 1, and by default is set to 0.5.
Higher values of <x> mean that hits that are fragments on their left (N
or 5'-terminal) side will be penalized less, but complete global alignments
will be penalized more. Lower values of <x> mean that fragments on the left
will be penalized more, and global alignments on this side will be favored.
This option only affects the configurations that allow local alignments,
e.g. -s and -f; unless one of these options is also activated, this option
has no effect. You have independent control over local/global alignment
behavior for the N/C (5'/3') termini of your target sequences using -swentry
- [-swexit <x> ] Controls the total probability that is distributed
to local exits from the model, versus ending an alignment at the end of
the model as in a global alignment. <x> is a probability from 0 to 1, and
by default is set to 0.5. Higher values of <x> mean that hits that are fragments
on their right (C or 3'-terminal) side will be penalized less, but complete
global alignments will be penalized more. Lower values of <x> mean that fragments
on the right will be penalized more, and global alignments on this side
will be favored. This option only affects the configurations that allow
local alignments, e.g. -s and -f; unless one of these options is also activated,
this option has no effect. You have independent control over local/global
alignment behavior for the N/C (5'/3') termini of your target sequences
using -swentry and -swexit.
- [-verbose ] Print more possibly useful stuff,
such as the individual scores for each sequence in the alignment.
] Use the BLOSUM filtering algorithm to weight the sequences, instead of
the default. Cluster the sequences at a given percentage identity (see
-idlevel); assign each cluster a total weight of 1.0, distributed equally
amongst the members of that cluster.
- [-wgsc ] Use the Gerstein/Sonnhammer/Chothia
ad hoc sequence weighting algorithm. This is already the default, so this
option has no effect (unless it follows another option in the -w family,
in which case it overrides it).
- [-wme ] Use the Krogh/Mitchison maximum entropy
algorithm to "weight" the sequences. This supercedes the Eddy/Mitchison/Durbin
maximum discrimination algorithm, which gives almost identical weights
but is less robust. ME weighting seems to give a marginal increase in
sensitivity over the default GSC weights, but takes a fair amount of time.
- [-wnone ] Turn off all sequence weighting.
- [-wvoronoi ] Use the Sibbald/Argos
Voronoi sequence weighting algorithm in place of the default GSC weighting.
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Up: Manual pages
Previous: hmmalign - align sequences
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