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HMMER(1)                         HMMER Manual                         HMMER(1)


NAME

       HMMER - profile HMMs for biological sequence analysis


SYNOPSIS

       hmmalign
         Align sequences to a profile

       hmmbuild
         Construct profile(s) from multiple sequence alignment(s)

       hmmconvert
         Convert profile file to various HMMER and non-HMMER formats

       hmmemit
         Sample sequences from a profile

       hmmfetch
         Retrieve profile HMM(s) from a file

       hmmpress
         Prepare an HMM database for hmmscan

       hmmscan
         Search sequence(s) against a profile database

       hmmsearch
         Search profile(s) against a sequence database

       hmmsim
         Collect profile score distributions on random sequences

       hmmstat
         Summary statistics for a profile file

       jackhmmer
         Iterative search of a protein sequence against a protein sequence
       database

       phmmer
         Search a protein sequence against a protein sequence database


DESCRIPTION

       HMMER is a suite of several programs for biological sequence alignment
       and database homology search. It uses probabilistic models called
       "profile hidden Markov models" (profile HMMs) to represent the likely
       evolutionary homologs of a single sequence or a multiple alignment of a
       sequence family. A main avenue of research is to improve the
       evolutionary predictive models in HMMER to be able to recognize and
       accurately align increasingly remote homologs, distant in time.

       HMMER is also used as an organizational tool, to group the
       exponentially growing number of biological sequences into a vastly
       smaller set of well-annotated sequence families. New sequences can be
       annotated by comparison against curated sequence family databases of
       prebuilt HMMER profiles, in addition or instead of comparison to the
       entire sequence database. Databases such as Pfam, SMART, and TIGRfams,
       among others, are based on this principle.

       HMMER is used in three main modes: to search a sequence database for
       new homologs of a sequence or a sequence family; to search a profile
       database (like Pfam) to find what known family a query sequence belongs
       to, or what domains it has; and to automatically construct large
       multiple alignments (i.e. with an effectively unlimited number of
       sequences) using a profile representative of a sequence family.

       Suppose you have a multiple sequence alignment of a sequence family of
       interest, and you want to search a sequence database for additional
       homologs. The hmmbuild program builds profile(s) from multiple
       alignment(s).  The hmmsearch program searches profile(s) against a
       sequence database.

       Suppose you have a single sequence of interest, and you want to search
       a sequence database for additional homologs. The phmmer program
       searches a single protein sequence against a protein sequence database.
       The jackhmmer program does the same thing but iteratively -- homologs
       detected in a previous round are incorporated into a new profile, and
       the new profile is searched again.  phmmer is used like BLASTP, and
       jackhmmer is used like a protein PSI-BLAST. Currently these two
       programs support only protein/protein comparison, but this will change
       with time.

       Suppose you have sequence(s) that you want to analyze using a HMMER-
       based profile HMM database like Pfam (http://pfam.sanger.ac.uk).  The
       hmmpress program formats a profile HMM flatfile (such as the file you
       would download from Pfam) into a HMMER binary database.  The hmmscan
       program searches sequence(s) against that database.

       Suppose you want to align lots of sequences. You can construct a
       manageably small alignment of a representative set of sequences, build
       a profile with hmmbuild, and use the hmmalign program to align any
       number of sequences to that profile.

       HMMER also includes some auxiliary tools for working with large profile
       databases.  hmmfetch fetches one or more profiles from a database.
       hmmstat prints summary statistics about a profile file.

       For compatibility with other profile software and previous versions of
       HMMER, the hmmconvert program converts profiles to a few other formats.
       We intend to add more support for other formats over time.

       The hmmemit program generates (simulates) "homologous" sequences by
       sampling from a profile. It can also generate a "consensus" sequence.

       The hmmsim program is a simulator used for collecting statistics about
       score distributions on random sequences.

       Each program has its own man page.


SEE ALSO

       This is a summary man page for the entire HMMER3 package.  See
       individual man pages [hmmbuild(1), for example] for usage, options, and
       description of each program in the package.

       For complete documentation, see the user guide that came with your
       HMMER distribution (Userguide.pdf); or see the HMMER web page
       (@HMMER_URL@).


COPYRIGHT

       @HMMER_COPYRIGHT@
       @HMMER_LICENSE@

       For additional information on copyright and licensing, see the file
       called COPYRIGHT in your HMMER source distribution, or see the HMMER
       web page (@HMMER_URL@).


AUTHOR

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147 USA
       http://eddylab.org

HMMER @HMMER_VERSION@            @HMMER_DATE@                         HMMER(1)

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