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 hmmpress
26 Prepare an HMM database for hmmscan
27 hmmscan
29 Search sequence(s) against a profile database
30 hmmsearch
32 Search profile(s) against a sequence database
33 hmmsim
35 Collect profile score distributions on random sequences
36 hmmstat
38 Summary statistics for a profile file
39 jackhmmer
41 Iterative search of a protein sequence against a protein sequence
42 database
43 phmmer
45 Search a protein sequence against a protein sequence database
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50 HMMER is a suite of several programs for biological sequence alignment
51 and database homology search. It uses probabilistic models called "pro‐
52 file hidden Markov models" (profile HMMs) to represent the likely evo‐
53 lutionary homologs of a single sequence or a multiple alignment of a
54 sequence family. A main avenue of research is to improve the evolution‐
55 ary predictive models in HMMER to be able to recognize and accurately
56 align increasingly remote homologs, distant in time.
57 HMMER is also used as an organizational tool, to group the exponen‐
59 tially growing number of biological sequences into a vastly smaller set
60 of well-annotated sequence families. New sequences can be annotated by
61 comparison against curated sequence family databases of prebuilt HMMER
62 profiles, in addition or instead of comparison to the entire sequence
63 database. Databases such as Pfam, SMART, and TIGRfams, among others,
64 are based on this principle.
65 HMMER is used in three main modes: to search a sequence database for
67 new homologs of a sequence or a sequence family; to search a profile
68 database (like Pfam) to find what known family a query sequence belongs
69 to, or what domains it has; and to automatically construct large multi‐
70 ple alignments (i.e. with an effectively unlimited number of sequences)
71 using a profile representative of a sequence family.
72 Suppose you have a multiple sequence alignment of a sequence family of
75 interest, and you want to search a sequence database for additional
76 homologs. The hmmbuild program builds profile(s) from multiple align‐
77 ment(s). The hmmsearch program searches profile(s) against a sequence
78 database.
79 Suppose you have a single sequence of interest, and you want to search
81 a sequence database for additional homologs. The phmmer program
82 searches a single protein sequence against a protein sequence database.
83 The jackhmmer program does the same thing but iteratively -- homologs
84 detected in a previous round are incorporated into a new profile, and
85 the new profile is searched again. phmmer is used like BLASTP, and
86 jackhmmer is used like a protein PSI-BLAST. Currently these two pro‐
87 grams support only protein/protein comparison, but this will change
88 with time.
89 Suppose you have sequence(s) that you want to analyze using a HMMER-
91 based profile HMM database like Pfam (http://pfam.sanger.ac.uk). The
92 hmmpress program formats a profile HMM flatfile (such as the file you
93 would download from Pfam) into a HMMER binary database. The hmmscan
94 program searches sequence(s) against that database.
95 Suppose you want to align lots of sequences. You can construct a man‐
97 ageably small alignment of a representative set of sequences, build a
98 profile with hmmbuild, and use the hmmalign program to align any number
99 of sequences to that profile.
100 HMMER also includes some auxiliary tools for working with large profile
102 databases. hmmfetch fetches one or more profiles from a database.
103 hmmstat prints summary statistics about a profile file.
104 For compatibility with other profile software and previous versions of
106 HMMER, the hmmconvert program converts profiles to a few other formats.
107 We intend to add more support for other formats over time.
108 The hmmemit program generates (simulates) "homologous" sequences by
110 sampling from a profile. It can also generate a "consensus" sequence.
111 The hmmsim program is a simulator used for collecting statistics about
113 score distributions on random sequences.
114 Each program has its own man page.
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120 This is a summary man page for the entire HMMER3 package. See individ‐
121 ual man pages [hmmbuild(1), for example] for usage, options, and
122 description of each program in the package.
123 For complete documentation, see the user guide that came with your
126 HMMER distribution (Userguide.pdf); or see the HMMER web page
127 (@HMMER_URL@).
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132 @HMMER_COPYRIGHT@
133 @HMMER_LICENSE@
134 For additional information on copyright and licensing, see the file
136 called COPYRIGHT in your HMMER source distribution, or see the HMMER
137 web page (@HMMER_URL@).
138
142 Eddy/Rivas Laboratory
143 Janelia Farm Research Campus
144 19700 Helix Drive
145 Ashburn VA 20147 USA
146 http://eddylab.org
147HMMER @HMMER_VERSION@ @HMMER_DATE@ HMMER(1)