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 accu-
       rately 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 for-
       mats. 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)