1HMMER(1)                         HMMER Manual                         HMMER(1)
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NAME

6       HMMER - profile HMMs for biological sequence analysis
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SYNOPSIS

10       hmmalign
11         Align sequences to a profile
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13       hmmbuild
14         Construct profiles from multiple sequence alignments
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16       hmmconvert
17         Convert profile file to various formats
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19       hmmemit
20         Sample sequences from a profile
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22       hmmfetch
23         Retrieve profiles from a file
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25       hmmlogo
26         Produce a conservation logo graphic from a profile
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28       hmmpgmd
29         Daemon for database search web services
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31       hmmpress
32         Prepare a profile database for hmmscan
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34       hmmscan
35         Search sequence(s) against a profile database
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37       hmmsearch
38         Search profile(s) against a sequence database
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40       hmmsim
41         Collect profile score distributions on random sequences
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43       hmmstat
44         Summary statistics for a profile file
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46       jackhmmer
47         Iteratively search sequence(s) against a sequence database
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49       makehmmerdb
50         build nhmmer database from a sequence file
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52       nhmmer
53         Search DNA/RNA queries against a DNA/RNA sequence database
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55       nhmmscan
56         Search DNA/RNA sequence(s) against a DNA/RNA profile database
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58       phmmer
59         Search protein sequence(s) against a protein sequence database
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61       alimask
62         Calculate and add column mask to a multiple sequence alignment
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DESCRIPTION

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.
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74       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.
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82       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.
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90       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.
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97       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.
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106       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).
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116       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.
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121       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.
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125       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.
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129       The hmmemit program generates  (simulates)  "homologous"  sequences  by
130       sampling from a profile. It can also generate a "consensus" sequence.
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132       The  hmmsim program is a simulator used for collecting statistics about
133       score distributions on random sequences.
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135       Each program has its own man page.
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SEE ALSO

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.
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145       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.
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155       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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AUTHOR

162       http://eddylab.org
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166HMMER 3.3.2                        Nov 2020                           HMMER(1)
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