1alimask(1) HMMER Manual alimask(1)
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6 alimask - calculate and add column mask to a multiple sequence align‐
7 ment
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11 alimask [options] msafile postmsafile
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16 alimask is used to apply a mask line to a multiple sequence alignment,
17 based on provided alignment or model coordinates. When hmmbuild re‐
18 ceives a masked alignment as input, it produces a profile model in
19 which the emission probabilities at masked positions are set to match
20 the background frequency, rather than being set based on observed fre‐
21 quencies in the alignment. Position-specific insertion and deletion
22 rates are not altered, even in masked regions. alimask autodetects in‐
23 put format, and produces masked alignments in Stockholm format.
24 msafile may contain only one sequence alignment.
25 A common motivation for masking a region in an alignment is that the
28 region contains a simple tandem repeat that is observed to cause an un‐
29 acceptably high rate of false positive hits.
30 In the simplest case, a mask range is given in coordinates relative to
33 the input alignment, using --alirange <s>. However it is more often
34 the case that the region to be masked has been identified in coordi‐
35 nates relative to the profile model (e.g. based on recognizing a simple
36 repeat pattern in false hit alignments or in the HMM logo). Not all
37 alignment columns are converted to match state positions in the profile
38 (see the --symfrac flag for hmmbuild for discussion), so model posi‐
39 tions do not necessarily match up to alignment column positions. To
40 remove the burden of converting model positions to alignment positions,
41 alimask accepts the mask range input in model coordinates as well, us‐
42 ing --modelrange <s>. When using this flag, alimask determines which
43 alignment positions would be identified by hmmbuild as match states, a
44 process that requires that all hmmbuild flags impacting that decision
45 be supplied to alimask. It is for this reason that many of the hmm‐
46 build flags are also used by alimask.
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52 -h Help; print a brief reminder of command line usage and all
53 available options.
54 -o <f> Direct the summary output to file <f>, rather than to stdout.
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61 A single mask range is given as a dash-separated pair, like --model‐
62 range 10-20 and multiple ranges may be submitted as a comma-separated
63 list, --modelrange 10-20,30-42.
64 --modelrange <s>
68 Supply the given range(s) in model coordinates.
69 --alirange <s>
72 Supply the given range(s) in alignment coordinates.
73 --apendmask
76 Add to the existing mask found with the alignment. The default
77 is to overwrite any existing mask.
78 --model2ali <s>
81 Rather than actually produce the masked alignment, simply print
82 model range(s) corresponding to input alignment range(s).
83 --ali2model <s>
86 Rather than actually produce the masked alignment, simply print
87 alignment range(s) corresponding to input model range(s).
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92 --amino
93 Assert that sequences in msafile are protein, bypassing alphabet
94 autodetection.
95 --dna Assert that sequences in msafile are DNA, bypassing alphabet au‐
98 todetection.
99 --rna Assert that sequences in msafile are RNA, bypassing alphabet au‐
102 todetection.
103
108 These options control how consensus columns are defined in an align‐
109 ment.
110 --fast Define consensus columns as those that have a fraction >= sym‐
113 frac of residues as opposed to gaps. (See below for the --sym‐
114 frac option.) This is the default.
115 --hand Define consensus columns in next profile using reference annota‐
118 tion to the multiple alignment. This allows you to define any
119 consensus columns you like.
120 --symfrac <x>
123 Define the residue fraction threshold necessary to define a con‐
124 sensus column when using the --fast option. The default is 0.5.
125 The symbol fraction in each column is calculated after taking
126 relative sequence weighting into account, and ignoring gap char‐
127 acters corresponding to ends of sequence fragments (as opposed
128 to internal insertions/deletions). Setting this to 0.0 means
129 that every alignment column will be assigned as consensus, which
130 may be useful in some cases. Setting it to 1.0 means that only
131 columns that include 0 gaps (internal insertions/deletions) will
132 be assigned as consensus.
133 --fragthresh <x>
136 We only want to count terminal gaps as deletions if the aligned
137 sequence is known to be full-length, not if it is a fragment
138 (for instance, because only part of it was sequenced). HMMER
139 uses a simple rule to infer fragments: if the sequence length L
140 is less than or equal to a fraction <x> times the alignment
141 length in columns, then the sequence is handled as a fragment.
142 The default is 0.5. Setting --fragthresh 0 will define no
143 (nonempty) sequence as a fragment; you might want to do this if
144 you know you've got a carefully curated alignment of full-length
145 sequences. Setting --fragthresh 1 will define all sequences as
146 fragments; you might want to do this if you know your alignment
147 is entirely composed of fragments, such as translated short
148 reads in metagenomic shotgun data.
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153 HMMER uses an ad hoc sequence weighting algorithm to downweight closely
154 related sequences and upweight distantly related ones. This has the ef‐
155 fect of making models less biased by uneven phylogenetic representa‐
156 tion. For example, two identical sequences would typically each receive
157 half the weight that one sequence would. These options control which
158 algorithm gets used.
159 --wpb Use the Henikoff position-based sequence weighting scheme
162 [Henikoff and Henikoff, J. Mol. Biol. 243:574, 1994]. This is
163 the default.
164 --wgsc Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Ger‐
167 stein et al, J. Mol. Biol. 235:1067, 1994].
168 --wblosum
171 Use the same clustering scheme that was used to weight data in
172 calculating BLOSUM subsitution matrices [Henikoff and Henikoff,
173 Proc. Natl. Acad. Sci 89:10915, 1992]. Sequences are single-
174 linkage clustered at an identity threshold (default 0.62; see
175 --wid) and within each cluster of c sequences, each sequence
176 gets relative weight 1/c.
177 --wnone
180 No relative weights. All sequences are assigned uniform weight.
181 --wid <x>
184 Sets the identity threshold used by single-linkage clustering
185 when using --wblosum. Invalid with any other weighting scheme.
186 Default is 0.62.
187
194 --informat <s>
195 Assert that input msafile is in alignment format <s>, bypassing
196 format autodetection. Common choices for <s> include: stock‐
197 holm, a2m, afa, psiblast, clustal, phylip. For more informa‐
198 tion, and for codes for some less common formats, see main docu‐
199 mentation. The string <s> is case-insensitive (a2m or A2M both
200 work).
201 --outformat <s>
205 Write the output postmsafile in alignment format <s>. Common
206 choices for <s> include: stockholm, a2m, afa, psiblast, clustal,
207 phylip. The string <s> is case-insensitive (a2m or A2M both
208 work). Default is stockholm.
209 --seed <n>
213 Seed the random number generator with <n>, an integer >= 0. If
214 <n> is nonzero, any stochastic simulations will be reproducible;
215 the same command will give the same results. If <n> is 0, the
216 random number generator is seeded arbitrarily, and stochastic
217 simulations will vary from run to run of the same command. The
218 default seed is 42.
219
224 See hmmer(1) for a master man page with a list of all the individual
225 man pages for programs in the HMMER package.
226 For complete documentation, see the user guide that came with your HM‐
229 MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
230 mer.org/).
231
236 Copyright (C) 2020 Howard Hughes Medical Institute.
237 Freely distributed under the BSD open source license.
238 For additional information on copyright and licensing, see the file
240 called COPYRIGHT in your HMMER source distribution, or see the HMMER
241 web page (http://hmmer.org/).
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246 http://eddylab.org
247HMMER 3.3.2 Nov 2020 alimask(1)