1alimask(1) HMMER Manual alimask(1)
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6 alimask - Add mask line to a multiple sequence alignment
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10 alimask [options] <msafile> <postmsafile>
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15 alimask is used to apply a mask line to a multiple sequence alignment,
16 based on provided alignment or model coordinates. When hmmbuild
17 receives a masked alignment as input, it produces a profile model in
18 which the emission probabilities at masked positions are set to match
19 the background frequency, rather than being set based on observed fre‐
20 quencies in the alignment. Position-specific insertion and deletion
21 rates are not altered, even in masked regions. alimask autodetects
22 input format, and produces masked alignments in Stockholm format.
23 <msafile> may contain only one sequence alignment.
24 A common motivation for masking a region in an alignment is that the
27 region contains a simple tandem repeat that is observed to cause an
28 unacceptably high rate of false positive hits.
29 In the simplest case, a mask range is given in coordinates relative to
32 the input alignment, using --alirange <s>. However it is more often
33 the case that the region to be masked has been identified in coordi‐
34 nates relative to the profile model (e.g. based on recognizing a simple
35 repeat pattern in false hit alignments or in the HMM logo). Not all
36 alignment columns are converted to match state positions in the profile
37 (see the --symfrac flag for hmmbuild for discussion), so model posi‐
38 tions do not necessarily match up to alignment column positions. To
39 remove the burden of converting model positions to alignment positions,
40 alimask accepts the mask range input in model coordinates as well,
41 using --modelrange <s>. When using this flag, alimask determines which
42 alignment positions would be identified by hmmbuild as match states, a
43 process that requires that all hmmbuild flags impacting that decision
44 be supplied to alimask. It is for this reason that many of the hmm‐
45 build flags are also used by alimask.
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51 -h Help; print a brief reminder of command line usage and all
52 available options.
53 -o <f> Direct the summary output to file <f>, rather than to stdout.
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60 A single mask range is given as a dash-separated pair, like --model‐
61 range 10-20 and multiple ranges may be submitted as a comma-separated
62 list, --modelrange 10-20,30-42.
63 --modelrange <s>
67 Supply the given range(s) in model coordinates.
68 --alirange <s>
71 Supply the given range(s) in alignment coordinates.
72 --apendmask
75 Add to the existing mask found with the alignment. The default
76 is to overwrite any existing mask.
77 --model2ali <s>
80 Rather than actually produce the masked alignment, simply print
81 model range(s) corresponding to input alignment range(s).
82 --ali2model <s>
85 Rather than actually produce the masked alignment, simply print
86 alignment range(s) corresponding to input model range(s).
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91 The alphabet type (amino, DNA, or RNA) is autodetected by default, by
92 looking at the composition of the msafile. Autodetection is normally
93 quite reliable, but occasionally alphabet type may be ambiguous and
94 autodetection can fail (for instance, on tiny toy alignments of just a
95 few residues). To avoid this, or to increase robustness in automated
96 analysis pipelines, you may specify the alphabet type of msafile with
97 these options.
98 --amino
101 Specify that all sequences in msafile are proteins.
102 --dna Specify that all sequences in msafile are DNAs.
105 --rna Specify that all sequences in msafile are RNAs.
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113 These options control how consensus columns are defined in an align‐
114 ment.
115 --fast Define consensus columns as those that have a fraction >= sym‐
118 frac of residues as opposed to gaps. (See below for the --sym‐
119 frac option.) This is the default.
120 --hand Define consensus columns in next profile using reference annota‐
123 tion to the multiple alignment. This allows you to define any
124 consensus columns you like.
125 --symfrac <x>
128 Define the residue fraction threshold necessary to define a con‐
129 sensus column when using the --fast option. The default is 0.5.
130 The symbol fraction in each column is calculated after taking
131 relative sequence weighting into account, and ignoring gap char‐
132 acters corresponding to ends of sequence fragments (as opposed
133 to internal insertions/deletions). Setting this to 0.0 means
134 that every alignment column will be assigned as consensus, which
135 may be useful in some cases. Setting it to 1.0 means that only
136 columns that include 0 gaps (internal insertions/deletions) will
137 be assigned as consensus.
138 --fragthresh <x>
141 We only want to count terminal gaps as deletions if the aligned
142 sequence is known to be full-length, not if it is a fragment
143 (for instance, because only part of it was sequenced). HMMER
144 uses a simple rule to infer fragments: if the sequence length L
145 is less than or equal to a fraction <x> times the alignment
146 length in columns, then the sequence is handled as a fragment.
147 The default is 0.5. Setting --fragthresh0 will define no
148 (nonempty) sequence as a fragment; you might want to do this if
149 you know you've got a carefully curated alignment of full-length
150 sequences. Setting --fragthresh1 will define all sequences as
151 fragments; you might want to do this if you know your alignment
152 is entirely composed of fragments, such as translated short
153 reads in metagenomic shotgun data.
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158 HMMER uses an ad hoc sequence weighting algorithm to downweight closely
159 related sequences and upweight distantly related ones. This has the
160 effect of making models less biased by uneven phylogenetic representa‐
161 tion. For example, two identical sequences would typically each receive
162 half the weight that one sequence would. These options control which
163 algorithm gets used.
164 --wpb Use the Henikoff position-based sequence weighting scheme
167 [Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994]. This is
168 the default.
169 --wgsc Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Ger‐
172 stein et al, J. Mol. Biol. 235:1067, 1994].
173 --wblosum
176 Use the same clustering scheme that was used to weight data in
177 calculating BLOSUM subsitution matrices [Henikoff and Henikoff,
178 Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-
179 linkage clustered at an identity threshold (default 0.62; see
180 --wid) and within each cluster of c sequences, each sequence
181 gets relative weight 1/c.
182 --wnone
185 No relative weights. All sequences are assigned uniform weight.
186 --wid <x>
189 Sets the identity threshold used by single-linkage clustering
190 when using --wblosum. Invalid with any other weighting scheme.
191 Default is 0.62.
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199 --informat <s>
200 Declare that the input msafile is in format <s>. Currently the
201 accepted multiple alignment sequence file formats include Stock‐
202 holm, Aligned FASTA, Clustal, NCBI PSI-BLAST, PHYLIP, Selex, and
203 UCSC SAM A2M. Default is to autodetect the format of the file.
204 --seed <n>
208 Seed the random number generator with <n>, an integer >= 0. If
209 <n> is nonzero, any stochastic simulations will be reproducible;
210 the same command will give the same results. If <n> is 0, the
211 random number generator is seeded arbitrarily, and stochastic
212 simulations will vary from run to run of the same command. The
213 default seed is 42.
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219 See hmmer(1) for a master man page with a list of all the individual
220 man pages for programs in the HMMER package.
221 For complete documentation, see the user guide that came with your
224 HMMER distribution (Userguide.pdf); or see the HMMER web page ().
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230 Copyright (C) 2015 Howard Hughes Medical Institute.
231 Freely distributed under the GNU General Public License (GPLv3).
232 For additional information on copyright and licensing, see the file
234 called COPYRIGHT in your HMMER source distribution, or see the HMMER
235 web page ().
236
240 Eddy/Rivas Laboratory
241 Janelia Farm Research Campus
242 19700 Helix Drive
243 Ashburn VA 20147 USA
244 http://eddylab.org
245HMMER 3.1b2 February 2015 alimask(1)