1HMMER(1)                         HMMER Manual                         HMMER(1)
2
3
4

NAME

6       HMMER - profile HMMs for biological sequence analysis
7
8

SYNOPSIS

10       hmmalign
11         Align sequences to a profile
12
13       hmmbuild
14         Construct profile(s) from multiple sequence alignment(s)
15
16       hmmconvert
17         Convert profile file to various HMMER and non-HMMER formats
18
19       hmmemit
20         Sample sequences from a profile
21
22       hmmfetch
23         Retrieve profile HMM(s) from a file
24
25       hmmpgmd
26         Daemon  used  for  hmmer.org web server, for phmmer-, hmmsearch-, and
27       hmmscan-like search
28
29       hmmpress
30         Prepare an HMM database for hmmscan
31
32       hmmscan
33         Search protein sequence(s) against a protein profile database
34
35       hmmsearch
36         Search protein profile(s) against a protein sequence database
37
38       hmmsim
39         Collect profile score distributions on random sequences
40
41       hmmstat
42         Summary statistics for a profile file
43
44       jackhmmer
45         Iterative search of a protein sequence  against  a  protein  sequence
46       database
47
48       nhmmer
49         Search  nucleotide sequence(s), alignment(s), or profile(s) against a
50       nucleotide sequence database
51
52       nhmmscan
53         Search nucleotide sequence(s) against a nucleotide profile database
54
55       phmmer
56         Search a protein sequence(s) against a protein sequence database
57
58
59

DESCRIPTION

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
69       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
77       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
84
85       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
92       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
101       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
110
111       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
116       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
120       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
124       The  hmmemit  program  generates  (simulates) "homologous" sequences by
125       sampling from a profile. It can also generate a "consensus" sequence.
126
127       The hmmsim program is a simulator used for collecting statistics  about
128       score distributions on random sequences.
129
130       Each program has its own man page.
131
132
133

SEE ALSO

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
139
140       For  complete  documentation,  see  the  user guide that came with your
141       HMMER distribution (Userguide.pdf); or see the HMMER web page ().
142
143
144
146       Copyright (C) 2015 Howard Hughes Medical Institute.
147       Freely distributed under the GNU General Public License (GPLv3).
148
149       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
153
154

AUTHOR

156       Eddy/Rivas Laboratory
157       Janelia Farm Research Campus
158       19700 Helix Drive
159       Ashburn VA 20147 USA
160       http://eddylab.org
161
162
163
164HMMER 3.1b2                      February 2015                        HMMER(1)
Impressum