1HMMER(1) HMMER Manual HMMER(1)
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6 HMMER - profile HMMs for biological sequence analysis
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10 hmmalign
11 Align sequences to a profile
12 hmmbuild
14 Construct profile(s) from multiple sequence alignment(s)
15 hmmconvert
17 Convert profile file to various HMMER and non-HMMER formats
18 hmmemit
20 Sample sequences from a profile
21 hmmfetch
23 Retrieve profile HMM(s) from a file
24 hmmpgmd
26 Daemon used for hmmer.org web server, for phmmer-, hmmsearch-, and
27 hmmscan-like search
28 hmmpress
30 Prepare an HMM database for hmmscan
31 hmmscan
33 Search protein sequence(s) against a protein profile database
34 hmmsearch
36 Search protein profile(s) against a protein sequence database
37 hmmsim
39 Collect profile score distributions on random sequences
40 hmmstat
42 Summary statistics for a profile file
43 jackhmmer
45 Iterative search of a protein sequence against a protein sequence
46 database
47 nhmmer
49 Search nucleotide sequence(s), alignment(s), or profile(s) against a
50 nucleotide sequence database
51 nhmmscan
53 Search nucleotide sequence(s) against a nucleotide profile database
54 phmmer
56 Search a protein sequence(s) against a protein sequence database
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61 HMMER is a suite of several programs for biological sequence alignment
62 and database homology search. It uses probabilistic models called "pro‐
63 file hidden Markov models" (profile HMMs) to represent the likely evo‐
64 lutionary homologs of a single sequence or a multiple alignment of a
65 sequence family. A main avenue of research is to improve the evolution‐
66 ary predictive models in HMMER to be able to recognize and accurately
67 align increasingly remote homologs, distant in time.
68 HMMER is also used as an organizational tool, to group the exponen‐
70 tially growing number of biological sequences into a vastly smaller set
71 of well-annotated sequence families. New sequences can be annotated by
72 comparison against curated sequence family databases of prebuilt HMMER
73 profiles, in addition or instead of comparison to the entire sequence
74 database. Databases such as Pfam, SMART, and TIGRfams, among others,
75 are based on this principle.
76 HMMER is used in three main modes: to search a sequence database for
78 new homologs of a sequence or a sequence family; to search a profile
79 database (like Pfam) to find what known family a query sequence belongs
80 to, or what domains it has; and to automatically construct large multi‐
81 ple alignments (i.e. with an effectively unlimited number of sequences)
82 using a profile representative of a sequence family.
83 Suppose you have a multiple sequence alignment of a sequence family of
86 interest, and you want to search a sequence database for additional
87 homologs. The hmmbuild program builds profile(s) from multiple align‐
88 ment(s). The hmmsearch program searches protein profile(s) against a
89 protein sequence database, and nhmmer searches nucleotide profile(s)
90 against a nucleotide sequence database.
91 Suppose you have a single sequence of interest, and you want to search
93 a sequence database for additional homologs. The phmmer program
94 searches a single protein sequence against a protein sequence database.
95 The jackhmmer program does the same thing but iteratively -- homologs
96 detected in a previous round are incorporated into a new profile, and
97 the new profile is searched again. phmmer is used like BLASTP, and
98 jackhmmer is used like a protein PSI-BLAST. The nhmmer program searches
99 a single nucleotide sequence against a nucleotide sequence.
100 Suppose you have sequence(s) that you want to analyze using a HMMER-
102 based profile HMM database like Pfam (http://pfam.sanger.ac.uk). The
103 hmmpress program formats a profile HMM flatfile (such as the file you
104 would download from Pfam) into a HMMER binary database. The hmmscan
105 program searches protein sequence(s) against that database. The nhmm‐
106 scan program can similarly search nucleotide sequence(s) against a
107 pressed database of nucleotide profiles, such as from Dfam
108 (http://dfam.janelia.org).
109 Suppose you want to align lots of sequences. You can construct a man‐
112 ageably small alignment of a representative set of sequences, build a
113 profile with hmmbuild, and use the hmmalign program to align any number
114 of sequences to that profile.
115 HMMER also includes some auxiliary tools for working with large profile
117 databases. hmmfetch fetches one or more profiles from a database.
118 hmmstat prints summary statistics about a profile file.
119 For compatibility with other profile software and previous versions of
121 HMMER, the hmmconvert program converts profiles to a few other formats.
122 We intend to add more support for other formats over time.
123 The hmmemit program generates (simulates) "homologous" sequences by
125 sampling from a profile. It can also generate a "consensus" sequence.
126 The hmmsim program is a simulator used for collecting statistics about
128 score distributions on random sequences.
129 Each program has its own man page.
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135 This is a summary man page for the entire HMMER3 package. See individ‐
136 ual man pages [hmmbuild(1), for example] for usage, options, and
137 description of each program in the package.
138 For complete documentation, see the user guide that came with your
141 HMMER distribution (Userguide.pdf); or see the HMMER web page ().
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146 Copyright (C) 2015 Howard Hughes Medical Institute.
147 Freely distributed under the GNU General Public License (GPLv3).
148 For additional information on copyright and licensing, see the file
150 called COPYRIGHT in your HMMER source distribution, or see the HMMER
151 web page ().
152
156 Eddy/Rivas Laboratory
157 Janelia Farm Research Campus
158 19700 Helix Drive
159 Ashburn VA 20147 USA
160 http://eddylab.org
161HMMER 3.1b2 February 2015 HMMER(1)