1hmmer(1) HMMER Manual hmmer(1)
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6 HMMER - profile hidden Markov model software
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10 hmmalign
11 Align multiple sequences to a profile HMM.
12 hmmbuild
15 Build a profile HMM from a given multiple sequence alignment.
16 hmmcalibrate
19 Determine appropriate statistical significance parameters for a
20 profile HMM prior to doing database searches.
21 hmmconvert
24 Convert HMMER profile HMMs to other formats, such as GCG pro‐
25 files.
26 hmmemit
29 Generate sequences probabilistically from a profile HMM.
30 hmmfetch
33 Retrieve an HMM from an HMM database
34 hmmindex
37 Create a binary SSI index for an HMM database
38 hmmpfam
41 Search a profile HMM database with a sequence (i.e., annotate
42 various kinds of domains in the query sequence).
43 hmmsearch
46 Search a sequence database with a profile HMM (i.e., find addi‐
47 tional homologues of a modeled family).
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51 These programs use profile hidden Markov models (profile HMMs) to model
52 the primary structure consensus of a family of protein or nucleic acid
53 sequences.
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57 All HMMER programs give a brief summary of their command-line syntax
58 and options if invoked without any arguments. When invoked with the
59 single argument, -h (i.e., help), a program will report more verbose
60 command-line usage information, including rarely used, experimental,
61 and expert options. -h will report version numbers which are useful if
62 you need to report a bug or problem to me.
63 Each HMMER program has its own man page briefly summarizing command
66 line usage. There is also a user's guide that came with the software
67 distribution, which includes a tutorial introduction and more detailed
68 descriptions of the programs.
69 See http://hmmer.wustl.edu/ for on-line documentation and the current
71 HMMER release.
72 In general, no command line options should be needed by beginning
75 users. The defaults are set up for optimum performance in most situa‐
76 tions. Options that are single lowercase letters (e.g. -a ) are "com‐
77 mon" options that are expected to be frequently used and will be impor‐
78 tant in many applications. Options that are single uppercase letters
79 (e.g. -B ) are usually less common options, but also may be important
80 in some applications. Options that are full words (e.g. --verbose )
81 are either rarely used, experimental, or expert options. Some experi‐
82 mental options are only there for my own ongoing experiments with
83 HMMER, and may not be supported or documented adequately.
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88 In general, HMMER attempts to read most common biological sequence file
89 formats. It autodetects the format of the file. It also autodetects
90 whether the sequences are protein or nucleic acid. Standard IUPAC
91 degeneracy codes are allowed in addition to the usual 4-letter or
92 20-letter codes.
93 Unaligned sequences
96 Unaligned sequence files may be in FASTA, Swissprot, EMBL, Gen‐
97 Bank, PIR, Intelligenetics, Strider, or GCG format. These for‐
98 mats are documented in the User's Guide.
99 Sequence alignments
102 Multiple sequence alignments may be in CLUSTALW, SELEX, or GCG
103 MSF format. These formats are documented in the User's Guide.
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107 For ease of using large stable sequence and HMM databases, HMMER looks
108 for sequence files and HMM files in the current working directory as
109 well as in system directories specified by environment variables.
110 BLASTDB
113 Specifies the directory location of sequence databases. Example:
114 /seqlibs/blast-db/. In installations that use BLAST software,
115 this environment variable is likely to already be set.
116 HMMERDB
119 Specifies the directory location of HMM databases. Example:
120 /seqlibs/pfam/.
121HMMER 2.3.2 Oct 2003 hmmer(1)