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 profiles from multiple sequence alignments
15 hmmconvert
17 Convert profile file to various formats
18 hmmemit
20 Sample sequences from a profile
21 hmmfetch
23 Retrieve profiles from a file
24 hmmlogo
26 Produce a conservation logo graphic from a profile
27 hmmpgmd
29 Daemon for database search web services
30 hmmpress
32 Prepare a profile database for hmmscan
33 hmmscan
35 Search sequence(s) against a profile database
36 hmmsearch
38 Search profile(s) against a sequence database
39 hmmsim
41 Collect profile score distributions on random sequences
42 hmmstat
44 Summary statistics for a profile file
45 jackhmmer
47 Iteratively search sequence(s) against a sequence database
48 makehmmerdb
50 build nhmmer database from a sequence file
51 nhmmer
53 Search DNA/RNA queries against a DNA/RNA sequence database
54 nhmmscan
56 Search DNA/RNA sequence(s) against a DNA/RNA profile database
57 phmmer
59 Search protein sequence(s) against a protein sequence database
60 alimask
62 Calculate and add column mask to a multiple sequence alignment
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66 HMMER is a suite of several programs for biological sequence alignment
67 and database homology search. It uses probabilistic models called "pro‐
68 file hidden Markov models" (profile HMMs) to represent the likely evo‐
69 lutionary homologs of a single sequence or a multiple alignment of a
70 sequence family. A main avenue of research is to improve the evolution‐
71 ary predictive models in HMMER to be able to recognize and accurately
72 align increasingly remote homologs, distant in time.
73 HMMER is also used as an organizational tool, to group the exponen‐
75 tially growing number of biological sequences into a vastly smaller set
76 of well-annotated sequence families. New sequences can be annotated by
77 comparison against curated sequence family databases of prebuilt HMMER
78 profiles, in addition or instead of comparison to the entire sequence
79 database. Databases such as Pfam, SMART, and TIGRfams, among others,
80 are based on this principle.
81 HMMER is used in three main modes: to search a sequence database for
83 new homologs of a sequence or a sequence family; to search a profile
84 database (like Pfam) to find what known family a query sequence belongs
85 to, or what domains it has; and to automatically construct large multi‐
86 ple alignments (i.e. with an effectively unlimited number of sequences)
87 using a profile representative of a sequence family.
88 Suppose you have a multiple sequence alignment of a sequence family of
91 interest, and you want to search a sequence database for additional ho‐
92 mologs. The hmmbuild program builds profile(s) from multiple align‐
93 ment(s). The hmmsearch program searches protein profile(s) against a
94 protein sequence database, and nhmmer searches nucleotide profile(s)
95 against a nucleotide sequence database.
96 Suppose you have a single sequence of interest, and you want to search
98 a sequence database for additional homologs. The phmmer program
99 searches a single protein sequence against a protein sequence database.
100 The jackhmmer program does the same thing but iteratively -- homologs
101 detected in a previous round are incorporated into a new profile, and
102 the new profile is searched again. phmmer is used like BLASTP, and
103 jackhmmer is used like a protein PSI-BLAST. The nhmmer program searches
104 a single nucleotide sequence against a nucleotide sequence.
105 Suppose you have sequence(s) that you want to analyze using a HMMER-
107 based profile HMM database like Pfam (http://pfam.sanger.ac.uk). The
108 hmmpress program formats a profile HMM flatfile (such as the file you
109 would download from Pfam) into a HMMER binary database. The hmmscan
110 program searches protein sequence(s) against that database. The nhmm‐
111 scan program can similarly search nucleotide sequence(s) against a
112 pressed database of nucleotide profiles, such as from Dfam
113 (http://dfam.janelia.org).
114 Suppose you want to align lots of sequences. You can construct a man‐
117 ageably small alignment of a representative set of sequences, build a
118 profile with hmmbuild, and use the hmmalign program to align any number
119 of sequences to that profile.
120 HMMER also includes some auxiliary tools for working with large profile
122 databases. hmmfetch fetches one or more profiles from a database.
123 hmmstat prints summary statistics about a profile file.
124 For compatibility with other profile software and previous versions of
126 HMMER, the hmmconvert program converts profiles to a few other formats.
127 We intend to add more support for other formats over time.
128 The hmmemit program generates (simulates) "homologous" sequences by
130 sampling from a profile. It can also generate a "consensus" sequence.
131 The hmmsim program is a simulator used for collecting statistics about
133 score distributions on random sequences.
134 Each program has its own man page.
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140 This is a summary man page for the entire HMMER3 package. See individ‐
141 ual man pages [hmmbuild(1), for example] for usage, options, and de‐
142 scription of each program in the package.
143 For complete documentation, see the user guide that came with your HM‐
146 MER distribution (Userguide.pdf); or see the HMMER web page (http://hm‐
147 mer.org/).
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152 Copyright (C) 2020 Howard Hughes Medical Institute.
153 Freely distributed under the BSD open source license.
154 For additional information on copyright and licensing, see the file
156 called COPYRIGHT in your HMMER source distribution, or see the HMMER
157 web page (http://hmmer.org/).
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162 http://eddylab.org
163HMMER 3.3.2 Nov 2020 HMMER(1)