NAME¶
alimask - Add mask line to a multiple sequence alignment
SYNOPSIS¶
alimask [options] <msafile>
<postmsafile>
DESCRIPTION¶
alimask is used to apply a mask line to a multiple sequence alignment,
based on provided alignment or model coordinates. When
hmmbuild
receives a masked alignment as input, it produces a profile model in which the
emission probabilities at masked positions are set to match the background
frequency, rather than being set based on observed frequencies in the
alignment. Position-specific insertion and deletion rates are not altered,
even in masked regions.
alimask autodetects input format, and produces
masked alignments in Stockholm format.
<msafile> may contain only
one sequence alignment.
A common motivation for masking a region in an alignment is that the region
contains a simple tandem repeat that is observed to cause an unacceptably high
rate of false positive hits.
In the simplest case, a mask range is given in coordinates relative to the input
alignment, using
--alirange <s>. However it is more
often the case that the region to be masked has been identified in coordinates
relative to the profile model (e.g. based on recognizing a simple repeat
pattern in false hit alignments or in the HMM logo). Not all alignment columns
are converted to match state positions in the profile (see the
--symfrac flag for
hmmbuild for discussion), so model positions
do not necessarily match up to alignment column positions. To remove the
burden of converting model positions to alignment positions,
alimask
accepts the mask range input in model coordinates as well, using
--modelrange <s>. When using this flag,
alimask determines which alignment positions would be identified by
hmmbuild as match states, a process that requires that all
hmmbuild flags impacting that decision be supplied to
alimask.
It is for this reason that many of the
hmmbuild flags are also used by
alimask.
OPTIONS¶
- -h
- Help; print a brief reminder of command line usage and all available
options.
- -o <f>
- Direct the summary output to file <f>, rather than to
stdout.
OPTIONS FOR SPECIFYING MASK RANGE¶
A single mask range is given as a dash-separated pair, like
--modelrange
10-20 and multiple ranges may be submitted as a comma-separated list,
--modelrange 10-20,30-42.
- --modelrange <s>
- Supply the given range(s) in model coordinates.
- --alirange <s>
- Supply the given range(s) in alignment coordinates.
- --apendmask
- Add to the existing mask found with the alignment. The default is to
overwrite any existing mask.
- --model2ali <s>
- Rather than actually produce the masked alignment, simply print model
range(s) corresponding to input alignment range(s).
- --ali2model <s>
- Rather than actually produce the masked alignment, simply print alignment
range(s) corresponding to input model range(s).
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 --fast option. The default 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 include 0 gaps (internal insertions/deletions) 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 or equal to a fraction
<x> times the alignment length in columns, then the sequence
is handled as a fragment. The default is 0.5. Setting
--fragthresh0 will define no (nonempty) sequence as a
fragment; you might want to do this if you know you've got a carefully
curated alignment of full-length sequences. Setting
--fragthresh1 will define all sequences as fragments; you
might want to do this if you know your alignment is entirely composed of
fragments, such as translated short reads in metagenomic shotgun data.
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.
OTHER OPTIONS¶
- --informat <s>
- Declare that the input msafile is in format <s>.
Currently the accepted multiple alignment sequence file formats include
Stockholm, Aligned FASTA, Clustal, NCBI PSI-BLAST, PHYLIP, Selex, and UCSC
SAM A2M. 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.
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 ().
COPYRIGHT¶
Copyright (C) 2013 Howard Hughes Medical Institute.
Freely distributed under the GNU General Public License (GPLv3).
For additional information on copyright and licensing, see the file called
COPYRIGHT in your HMMER source distribution, or see the HMMER web page ().
AUTHOR¶
Eddy/Rivas Laboratory
Janelia Farm Research Campus
19700 Helix Drive
Ashburn VA 20147 USA
http://eddylab.org